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I'm Kenny Flannery, living out of a backpack since 2007 — Travel light, often hitchhike, sharing advice and stories with words, a camera and a podcast.
Showing posts from June, 2011
Show all
June 19, 2011
Through Adelaide Towards the Outback - Australian Hitchhiking Loop (Part 3)
Ben dropped me off on the road after having had a great adventure with him and friends the day before when he'd picked me up hitchhikin…
June 13, 2011
Cruising Sand Dunes and Kissed Properly - Australian Hitchhiking Loop (Part 2)
Christian gave me a ride to the freeway after a brief trip into Melbourne, it was time to start the next and perhaps most memorable portion…
June 04, 2011
Mullum to Melbourne Orange Pill - Australian Hitchhiking Loop (Part 1)
Mandie dropped me off on the freeway outside of Mullumbimby, I was pointing south to begin my massive looping tour of Australia, Melbourne …
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If you suck at doing hair, this Conair cordless auto curler might be your next BFF
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Trending News
Physics Help Plx (plz provide answer and not formula) THX!!!!?
A 1.0-cm-diameter pipe widens to 2.0 cm, then narrows to 0.5 cm. Liquid flows through the first segment at a speed of 4.0m/s.
What is the speed in the second segment?
What is the speed in the third segment?
What is the volume flow rate through the pipe?
3 Answers
- VamanLv 74 months agoFavorite Answer
we must use r^2 v= constant. r is the radius and v is the velocity.
first condition gives 1/4*4=1. This remains a constant. In the second segment r=1. velocity =1 m/s. In the third segment (1/4)^2 v=1.
v=16 m/s. In the first segment it is 4 m/s, in the second it is 1 m/s, in the third it is 16 m/s.
- Login to reply the answers
- JOHNLv 74 months ago
Every second the same quantity of fluid must pass through every cross-section of the pipe.
Let u =4.0m/s, v, w be the fluid velocities in the 1cm, 2cm and 0.5cm sections of the pipe.
In 1s π(1/2)² x 400cm³ passes any 1cm diameter cross-section. For the 2cm section this is π(2/2)²v = π(1/2)² x 400, giving v = 100cm/s = 1m/s.
For the 0.5cm section this is π(0.5/2)²w = π(1/2)² x 400, giving w = 1600cm/s = 16m/s.
- Login to reply the answers
- Anonymous4 months ago
- Login to reply the answers


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by jonnigrl1
Siblings fight over the family estate
| Daria sat in the courtroom with a dark, grim look on her face. Her sister Ryan agreed to give their younger brother Oren their family estate as per their dead mother's request.
Their father, Jamie Wright, owned a house that sat on 100 acres of land in North Carolina. There were stocks and bonds along with several bank accounts so the family was well off.
His wife Anita became in charge of the estate and when she died a few months back, she left everything to their son Oren. Her daughters were not included in anything so Daria challenged her mom's will.
Daria and her mom Anita were never fond of each other. Anita was jealous of the close relationship that Daria had with her father, and Daria hated how Anita doted on Oren.
Their older sister Ryan went along with everything Oren did. She worshipped him and that made Daria furious. She couldn't understand how Ryan could agree to turn over the family estate to Oren but she did.
There were questions about Oren's biological father because he looked so much like a friend of the family named Jonas.
Every time Daria brought up and questioned who Oren's real father was, Ryan held up her hands and stormed away from her. She wanted no parts of the conversation although deep in her heart, she knew the questions were valid.
Ryan thought it was easier to get along with her siblings. Daria's thoughts were different because she was a fighter.
Daria watched with gritted teeth as her brother's and sister's lawyer tried to shut down her case for sharing the estate. She looked at Ryan with total disgust and out the corner of her eye, she could see Oren smirking.
The judge called for a two hour recess and Daria darted out of the courtroom like a bat out of hell. She had no conversation for her brother or sister so her best bet was to leave quickly.
As she sat on a bench in a corner of the court's hallway, she noticed Ryan approaching her.
Daria stood up quickly, held her hand up and said, "Nope, not today Ryan. I have nothing to say to you so turn around and go back to your brother!"
"Look, we need to talk Daria. This division has gone far enough. If mom wanted Oren to have control of the estate then so be it!"
"I disagree with you Ryan. Mom thought giving Oren everything was her way of getting back at our cheating father. She knew damn well Oren did not belong to him so she decided to give another man's son his estate."
"Daria don't say that!"
"No Ryan! It's time you face the fact that Oren is not our full biological brother and I intend to prove it. He will not get my father's full estate under false pretenses!"
"Let it go Daria. This is not what mom wanted!"
"To hell with what mom wanted. She was an evil, vindictive woman, but I'll show her. Oren will never see a dime of that money or enjoy the fruits of that land. He is not my father's child!"
Daria walked away from a shocked Ryan. Her mouth hung open as she watched her baby sister stomp through the halls like a mad woman.
Oren walked over to Ryan and just stared at her. He had never seen his older sister so sad and overwhelmed at the same time.
"Look Oren, we have to discuss this situation. It has gotten out of hand and frankly, I'm sick of it. We all need to meet in a room somewhere and hash this thing out!" said Ryan.
Oren looked at his older sister, turned on his heels, and ran down the hall after Daria.
He caught up with Daria, grabbed her by her arm and said, "We need to talk!"
"There's nothing to talk about Oren. You've made your decision and I've made mine. I will not allow you to take control of my father's estate."
"Okay. Let's just talk about this before we make anymore decisions in court."
Daria and Oren walked back to where Ryan was standing and found an empty room so they could talk.
"I never really wanted this estate but it's what the court document says Daria."
"But you don't have to abide by that document. You know what mom did wasn't right. There are three sibling involved so how in hell can she just award the whole estate to one?"
"Yeah but like I said, it's what mom wanted so why question it," said Oren.
"Because it's not right and you know it!"
Just then a knock on the door interrupted their discussion. A court officer handed Daria an envelope and told them that court would start in ten minutes.
"What's in the envelope," said Ryan.
"Never mind!" answered Daria
"Oren I think we all need to split this estate three ways. It's the right thing to do," said Ryan.
"Yeah alright, I'm tired of fighting, it's settled," said Oren.
As the three siblings made their way back to the courtroom, Daria opened the envelope and was astonished.
The other two didn't notice her reaction to the envelope because they were walking in front of her.
When the court proceedings began, Oren asked to drop everything. The judge agreed and everyone started filing out of the courtroom.
Daria grabbed Ryan's arm and showed her the document. Ryan looked at the document and stared in disbelief. She could not believe what she was seeing.
It turns out; a DNA test was done on all three siblings a while back, only to reveal that Ryan and Daria were not Jamie Wright's biological children. Oren was the only one that had Jamie Wright's blood flowing through his veins.
Ryan looked at Daria and said, "No good deed goes unpunished!"
Word Count =981


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Top photo: Pixabay, via. How long do you spend having sex? Probably varies, doesn't it.
The average bout of sex for British people lasts about 19 minutes, according to a recent survey of 4, people. That includes 10 minutes of foreplay and nine minutes of intercourse. The data was gathered by Lovehoney, an online sex toy shop, as part of an ongoing campaign to help couples orgasm together.
Read More You are doing amazing work! Thanks for sharing your wonderful tips.
Though we all like different things when it comes to our sex lives, it is possible to detect social trends in our desires. That's why dating site Saucy Dates decided to ask online respondents a couple of questions about sex — including how long they wanted intercourse to last. The website asked 3, people the following two questions: First, "The last time you had sex intercourse, not foreplayhow long did it last?
Vaginal sex typically lasts three to seven minutes, according to a Society for Sex Therapy and Research member survey. So how long should vaginal sex actually last? Many people consider the end of sex to be once all involved parties have climaxed.
According to a survey by sex toy company Love Honey, this is how long most couples spend on foreplay and sex. Of the customers surveyed by the company, the average time for a heterosexual couple was 19 minutes. As Vice points out, this is longer than the average found by other studies - possibly because buyers of sex toys may be more invested in spending more time on foreplay or sex generally.
Inappropriate intromission time causes sexual problems for couples, and therefore it is important for the couple to set treatment targets. We investigated appropriate intromission times by conducting a questionnaire survey of the interval from initiation of insertion to just before ejaculation in Japanese married couples. A questionnaire survey of married couples was conducted by mail.
Luckily we all have different likes and turn ons and we all derive sexual satisfaction in different ways, so the topic of the ideal duration for intercourse remains a fairly subjective one. InAmerican physician Dr. Irwin Goldstein conducted a survey of 1, couples to determine the average duration of their lovemaking sessions.
Back to Health A to Z. Premature ejaculation is the most common ejaculation problem. It's where the male ejaculates too quickly during sexual intercourse.


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Ami Magazine article. October 29http://www.localjewishnews.com/wp-content/uploads/2014/11/ami190_feature_HousingCrisis-2.pdf
Considering ?
shviger is there
How much less convenient is flying LGA-CAK instead of -CLE if I want to go to cleveland? I can rent a car if that would make things much easier.
How would you getting around CLE without a car?
This has nothing to do with CLE...Hidden city?Miles?


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Summer Lakes & Summer Park CE Class
Summer Lakes and Summer Park hosted a complimentary CE Class, Legal Update I, taught by Rob Cook, on Thursday, April 19th in the Drees Custom Homes model home.
Agents enjoyed breakfast, class and a chance to win door prizes compliments of the builders in Summer Lakes and Summer Park: Drees Custom Homes, Horizon Homes, J. Patrick Homes, and Plantation Homes. After the class, a complimentary lunch was served in the Plantation model home.
Congratulations to all the door prize winners:
- Alicia Arroyos with Gary Greene winner of the Gift basket from Drees
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Parliamentary team issues ultimatum on Ruring'u Stadium
Monday December 2 2019
The Parliamentary Committee in charge of sports has given the Sports Ministry a three-month ultimatum to address the stalemate in the construction of stadiums in the country.
Speaking at Ruring'u Stadium in Nyeri County, the committee chairman Victor Munyaka termed the status of Ruring'u Stadium 'a big shame.' Reconstruction work on the stadium was launched by President Uhuru Kenyatta three years ago.
"We are on a fact-finding mission to establish whether public money has been misused in all the stadiums which have stalled in the country. After this, we are going to recommend a thorough audit of what has been done through engineers and other experts who will give a report on the quality of work and if there is value for money," said Munyaka.
He added: "As a committee, we blame the Ministry of Sports and Sports Kenya who have the responsibility to do this job. We are also blaming the contractor because we have noted that there has been poor communication and coordination of the progress of work between him and the consultants who are even not here."
Going by the current status of the stadium and the money which has been disbursed already by the government, Munyaka said it was possible that money meant for constructing the stadium had been misused.
This inspection comes barely two weeks after Nyeri Town MP Ngunjiri Wambugu raised the red flag over the stadium. Ngunjiri called upon the government agencies to find out if money meant for the project had been squandered.
Ngunjiri, who had accompanied the committee during the inspection tour at the weekend, maintained his stand that the government should commission the National Youth Service and engineers from the military to take over work on the facility.
"The Kenyan youth is not interested in government bureaucracies as to who is holding the money or who is not doing this or that. All they want is a facility to train and grow their talents," said Ngunjiri.
Another committee member, Dan Wanyama, urged the President to intervene in the matter of the stalled stadiums in the country, adding that Sports Cabinet Secretary Amina Mohamed and Principal Secretary Kirimi Kaberia must be held to account.
"If the two are not able to perform this primary task, they should step aside and let other able Kenyans deliver this job. As of now, the Ministry of Sports cannot say it does not have money because 35 per cent of betting taxes are being channelled directly to their docket," lamented Wanyama.
He disclosed that the ministry is focused on high-end games like golf and motorsport, neglecting the common youth.


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The accurate interpretation of variation in Mendelian disease genes has lagged behind data generation as sequencing has become increasingly accessible. Ongoing large sequencing efforts present huge interpretive challenges, but they also provide an invaluable opportunity to characterize the spectrum and importance of rare variation.
We analyzed sequence data from 7,855 clinical cardiomyopathy cases and 60,706 Exome Aggregation Consortium (ExAC) reference samples to obtain a better understanding of genetic variation in a representative autosomal dominant disorder.
We found that in some genes previously reported as important causes of a given cardiomyopathy, rare variation is not clinically informative because there is an unacceptably high likelihood of false-positive interpretation. By contrast, in other genes, we find that diagnostic laboratories may be overly conservative when assessing variant pathogenicity.
We outline improved analytical approaches that evaluate which genes and variant classes are interpretable and propose that these will increase the clinical utility of testing across a range of Mendelian diseases.
Genet Med 19 2, 192–203.
Interpretation of rare genetic variation, whether in a clinical diagnostic or research setting, has not kept pace with the accelerating data generation using high-throughput DNA sequencing. Increasingly extensive gene panels, as well as whole-exome and genome sequencing, are used to interrogate the growing number of genes implicated in Mendelian diseases.1 However, such panels only modestly increase the number of high-confidence diagnostic results while identifying ever larger numbers of variants of uncertain significance2,3; these inconclusive results not only reduce the clinical utility of testing but also can lead to misinterpretation and misdiagnosis.
Central to the challenge of rare variant interpretation is the paradox that individually rare variants are now seen to be collectively common. Although it is accepted that a common variant can be excluded as a cause of a rare and penetrant Mendelian disease, the community has been slower to recognize that many rare variants identified in Mendelian disease genes are innocent bystanders and some "rare" variants are not rare at all. Recent population sequencing efforts have raised awareness of these issues (e.g., the 1000 Genomes Project,4 the Exome Sequencing Project (http://evs.gs.washington.edu/EVS), but the full extent is now revealed in the Exome Aggregation Consortium (ExAC) data set (http://exac.broadinstitute.org), in which the average exome contains 7.6 rare nonsynonymous variants (minor allele frequency (MAF) <0.1%) in well-characterized dominant disease genes, with the majority being very rare or "private."5 Clearly, only a small minority can actually cause a penetrant Mendelian disease.6
The challenges of variant interpretation in Mendelian disorders are particularly well illustrated by inherited cardiomyopathies: hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC). These largely autosomal dominant disorders are relatively common, genetically heterogeneous, and medically important;7 consequently, cardiomyopathy genes feature prominently in the American College of Medical Genetics and Genomics list of proposed genes to be routinely analyzed in all exome or genome sequencing.8 Although clinical genetic testing in cardiomyopathy has been available for more than a decade, the number of genes reported as disease-causing has increased dramatically in recent years, often without robust evidence.
Here, we leveraged two substantial resources to better understand and interpret rare variation in cardiomyopathy genes. We compared sequence data from 7,855 individuals who had a clinical diagnosis of cardiomyopathy with 60,706 reference samples from the ExAC consortium, the first data set powered to assess variant alleles present in the population at a range of 1:1,000–100,000 that might previously have been considered pathogenic yet may in fact be too common to cause penetrant Mendelian disease.
Through these analyses, we aimed to define the genes, regions of genes, and/or classes of variants that can be reliably interpreted in a clinical setting and in doing so enhance variant interpretation and increase clinical diagnostic yields.
Materials and Methods
Clinical and control cohorts
Data from 3,267 individuals with a clinical diagnosis of HCM, 559 with DCM, and 361 with ARVC were obtained from the Oxford Medical Genetics Laboratory for up to 16 genes for HCM, 28 genes for DCM, and 8 genes for ARVC (Supplementary Table S1a online). Data from Partners Laboratory of Molecular Medicine (LMM) were downloaded from the supplemental files of previous publications and included data from up to 18 genes sequenced in 632–2,912 HCM patients9 and up to 46 genes sequenced in 121–756 DCM patients3 (Supplementary Table S1b online). Because there were no significant differences in the proportion of cases of rare variants in each gene between the two laboratories (Fisher's exact test), the data were combined (Supplementary Table S3a,b online).
Data were downloaded from ExAC (http://exac.broadinstitute.org; version 0.3, January 2015). Only genes with a high proportion of coding regions covered to a median sequence depth of >30× and only high-quality (PASS filter) variants were included in our analyses. In addition, we adjusted the total number of ExAC samples per gene based on the mean coverage at the variant sites of interest.
Please refer to Supplementary Note S1 online for more detailed information on each component cohort.
Defining an allele frequency threshold for rare variation
The single most common confirmed pathogenic variant in both clinical cohorts was MYBPC3 c.1504C>T (p.Arg502Trp), which was found in 104/6,179 HCM cases (1.7%; 95 CI: 1.4–2.0%); this variant was only observed three times in ExAC (MAF 2.5 × 10−5). We therefore applied a MAF threshold of 1 × 10−4 as a conservative upper bound because variants more frequent than this in the general population would not be expected to be highly penetrant pathogenic mutations (see Supplementary Note S2 online). This MAF does not exclude the possibility of more common deleterious founder variants in specific populations where the genetic architecture of cardiomyopathy is not well defined.
Calculation of rare variant frequency in cardiomyopathy and ExAC cohorts
For each gene, the frequency of rare variants (MAF <1 × 10−4) in ExAC was calculated by dividing the sum of the adjusted allele count by the mean of the total adjusted alleles. The frequency of rare variation in the cardiomyopathy cohorts was calculated by dividing the sum of rare variants identified in cardiomyopathy cases by the total number of patients analyzed for each gene. Only likely protein-altering variants in designated canonical transcripts (Supplementary Table S2 online) were analyzed: missense, in-frame insertions/deletions, frameshift, nonsense, and variants affecting the splice donor and acceptor regions (first and last two bases of each intron). Analyses were performed for all protein-altering variants and separately for variants predicted to be nontruncating (missense and in-frame insertions and deletions) and truncating (frameshift, nonsense, splice donor/acceptor). To ensure that population-specific variants did not have a confounding effect on this analysis, we compared the results seen in the LMM DCM cohort for all samples and for Caucasians only (see Supplementary Note S4 online).
In total, after data from both clinical laboratories were combined and poorly covered genes in ExAC were excluded, 20 genes sequenced in 632–6,179 HCM patients, 46 genes sequenced in 121–1,315 DCM patients, and 8 genes sequenced in 93–361 ARVC patients were analyzed. See Supplementary Table S2 online for full details of cohort sizes for each gene.
Comparison of variation between cardiomyopathy and ExAC cohorts
For each gene, the frequency of rare variation in the clinical cohort was compared with that in ExAC. Case excess was defined by subtracting the proportion of individuals in ExAC with a filtered variant from the proportion in the clinical cohort. We made the simplifying assumption that the frequency of rare benign variants was equivalent in cases and ExAC, and that the frequency of pathogenic variants in ExAC is sufficiently low so as not to affect this comparison. A Fisher's exact test was performed to test the significance of observed excess in cases.
For each gene and variant class, we calculated two related metrics: the odds ratio (OR) with 95% confidence intervals and the etiological fraction (EF)10,11,12 (calculated as: (OR-1)/OR × 100; for further information on EF please refer to Supplementary Note S3 online). These metrics were calculated for all protein-altering variants and separately for predicted nontruncating and truncating subsets.
All statistical tests used in these analyses are two-sided, unless otherwise stated, and analysis was undertaken using Stata statistical analysis software (StataCorp. 2007. Stata Statistical Software: Release 10. College Station, TX: StataCorp LP.).
Distribution of missense variants in MYH7
To identify putative hotspots of pathogenic missense mutations in MYH7, distinct rare missense variants from the HCM, DCM, and ExAC cohorts were mapped along the protein sequence. Nonrandom mutation cluster (NMC),13 implemented in the iPAC Bioconductor R package, was used to identify clusters of variants in each cohort (R source code of NMC algorithm: https://bioconductor.org/packages/release/bioc/html/iPAC.html).
Analysis of research cardiomyopathy cohorts
Research cardiomyopathy cohorts are defined as published studies from research laboratories where patient samples were subjected to sequencing across panels of cardiac genes. The HCM research cohort14 sequenced 874 patients across 35 genes (12 associated primarily with HCM, 7 with DCM, 7 with ARVC, and 9 with arrhythmias, as stated by Lopes et al.). The DCM research cohort15,16,17 comprised 312–324 patients sequenced for 12 confirmed and putative DCM genes (not including TTN). Putative pathogenic variants in these studies are not identified by clinical-grade classification but rather by criteria such as variant type, population frequency, and in silico algorithm prediction—the details of the criteria used in each study are described in the published articles.
Rare variant frequencies and case excess were calculated for each gene as described for the clinical cohorts. The number of variants reported to be putatively pathogenic for each gene in these studies was compared with the number predicted to be pathogenic based on the case excess observed in these cohorts.
HGMD cardiomyopathy mutations in ExAC
Variants in the Human Genome Mutation Database (HGMD; professional version 2015.1) associated with HCM, DCM, or ARVC ("disease-causing mutations" with a HGMD tag of DM and DM?) were identified based on manual curation of the HGMD disease terms. The total allele frequency and count from ExAC were extracted for each variant. Polymorphisms (ExAC MAF >1 × 10−2) were removed from the analysis. The number of HGMD variants present in ExAC was calculated at any frequency and with MAF >1 × 10−4. The total number of ExAC alleles and the total number of ExAC individuals with HGMD-associated cardiomyopathy variants were also calculated for each disease. Additionally, the ExAC frequencies of HGMD cardiomyopathy variants previously observed only once in the Exome Sequencing Project were analyzed to assess how the enhanced resolution of ExAC can clarify previously uninterpretable variants.
Comparison of rare variation between cardiomyopathy cohorts and ExAC
Variants identified by sequencing of putative cardiomyopathy genes in cases (n = 7,855) were collated by disease and gene (Supplementary Table S1a,b online). We compared the burden of rare protein-altering variants (ExAC MAF <1 × 10−4) detected in 20 HCM genes, 48 DCM genes, and 8 ARVC genes in HCM, DCM, and ARVC cases, respectively, with the burden observed in ExAC. Predicted truncating and nontruncating variants were analyzed separately ( Table 1 and Supplementary Table S4a–c online).
As expected,18,19,20 rare variation in the two major HCM genes accounted for the majority of variation in HCM cases (MYBPC3, 19.0% of cases; MYH7, 14.2%). Rare variants were less numerous in other well-characterized HCM genes (TNNI3, TNNT2, TPM1, MYL2, MYL3, ACTC1, PLN) and phenocopy genes (GLA, LAMP2, PRKAG2) (≤2% cases per gene). For each of these genes there is a significant (P < 0.05 after Bonferroni correction) excess of variation in cases as compared with ExAC, thus confirming their association with disease ( Figure 1 and Table 1 and Supplementary Table S5a online). However, for several more recently reported HCM genes (TNNC121, MYOZ222, ACTN223, ANKRD124) there was no significant excess of rare genetic variation in these HCM cases.
DCM is highly genetically heterogeneous, with up to ~60 implicated genes.20,25,26 In the clinical cohorts, truncating variants in TTN were most common (14.6%), in accordance with our findings in large research cohorts.27,28 The prevalence of rare variants in other well-characterized DCM genes was modest (MYH7, 5.3%; LMNA, 4.4%; TNNT2, 2.9%; and TPM1, 1.9%) but significantly enriched compared with ExAC ( Figure 1 and Table 1 and Supplementary Table S5b online). However, with the exception of truncating variants in DSP (2.8%), there was limited burden and modest or no significant excess variation in the remaining 40 genes tested. In ARVC, the five major genes each showed significant excess in cases ( Table 1 and Supplementary Table S5c online).
Overall, the yield of pathogenic (P) and likely pathogenic (LP) variants was 32% for HCM, 13% for DCM (but note that TTN was only sequenced in one-third of samples), and 36% for ARVC. Of note, in the genes robustly supported by an excess of pathogenic and likely pathogenic variants, even variants of uncertain significance were seen in excess over ExAC, suggesting that clinical laboratories may be overly conservative ( Figure 1 ).
Interpretation of variation by gene and variant class
Many variants in confirmed disease genes can be interpreted with confidence based on cumulative experience (e.g., multiple occurrences of segregation in families, de novo mutations, founder variants) and/or functional insights (e.g., null alleles in haploinsufficient genes). However, our ability to evaluate the pathogenicity of novel variants depends on the signal-to-noise ratio. For each gene and variant class, we calculated two related metrics: the odds ratio (OR) (ratio of odds of cardiomyopathy comparing rare variant carriers with noncarriers) and the etiological fraction (EF), which is a commonly used measure in epidemiology10,11,12 that estimates the proportion of cases in which the exposure (in this case, a rare variant in a gene) was causal (see Supplementary Note S3 online).
These analyses reaffirm high ORs and EFs in key cardiomyopathy genes and also highlight a number of previously reported cardiomyopathy genes that show limited disease association when compared with a very large number of reference samples ( Figure 2 and Table 1 and Supplementary Table S5a–c online). As expected, many genes have divergent results for truncating as compared with nontruncating variants; for example, MYH7 has an OR of 1 (0.5–4.5) for truncating variants versus an OR of 12 (10.9–13.3) for nontruncating variants in HCM cases.
This observation confirms the widely accepted view that missense alleles of MYH7 act as dominant negatives in HCM whereas truncating variants are not pathogenic. In genes whose truncating alleles are disease-causing, ORs are typically higher owing to the lower rate of truncating variants in the population. As expected, truncating variation in MYBPC3 associates strongly with HCM (the result of haploinsufficiency29), but neither truncating nor nontruncating variants in MYBPC3 show a significant association with DCM (OR = 1.3 (0.8–1.8); EF = 0.21 (0–0.46)), which is a finding that fits with mechanistic insights but challenges some widely held viewpoints.15,30 Among the ARVC genes, truncating alleles are informative for four major genes (and particularly common for PKP2 and DSP), whereas nontruncating variants in these genes are difficult to interpret reliably ( Figure 2 and Table 1 and Supplementary Tables S4c and S5c online).
Using protein domain knowledge to improve variant interpretation
At the gene level, ORs for nontruncating variants are typically modest; in the absence of prior clinical experience or functional data, interpretation is often uncertain. This may be improved by considering protein topology because pathogenic variants often cluster in specific regions in cases.31,32 We evaluated the distribution of rare missense alleles in MYH7, which encodes a protein with well-characterized functional and structural domains to determine whether systematic analysis of variant distribution refines interpretation. Nonrandom mutation cluster analysis13 revealed a significant cluster (P < 3 × 10−15; false discovery rate q < 5 × 10−13) between residues 181 and 937 in HCM cases, whereas in ExAC variants were depleted in this region and instead clustered between residues 1,271 and 1,903 (P < 3 × 10−8; false discovery rate q < 4 × 10−5) ( Figure 3a ). These data more precisely define the boundaries of mutation-enriched and depleted zones that can be used to generate more discriminating EFs; for example, for rare variants in HCM patients, EFs range from 0.97 in the HCM cluster to 0.67 in the control cluster ( Figure 3a , b ).
Application of findings
To facilitate the application of these findings for research and clinical use, we provide an overview of the genetic landscape of cardiomyopathy as represented by patient referrals received by UK and US clinical testing laboratories. This shows the relative importance of cardiomyopathy genes within these patient populations (measured as a "case excess") and their interpretability (expressed as the etiological fraction) ( Figure 3b , c ). Furthermore, we have created a Web resource, Atlas of Cardiac Genetic Variation (http://cardiodb.org/ACGV), to aid those assessing the relevance of specific genes and classes of variants to cardiomyopathies.
Reassessing extended gene panel cardiomyopathy research studies
Several research studies14,15,17,30 using extended gene panels have reported genetic overlap between diverse cardiac diseases that appear at odds with known disease mechanisms. We surmise that many such studies have not adequately accounted for background genetic variation, have relied on variant data from incompletely annotated disease-centered databases, and have not used segregation. Here, using ExAC data, we present a reanalysis of two representative research studies.14,15,16,17
In the research HCM cases, the excess variation in the known HCM genes (e.g., MYBPC3, MYH7) is substantial. By contrast, the measured variation in DCM, ARVC, and ion channel genes in the HCM patients—although also substantial—is similar to that seen in ExAC with little, if any, excess burden ( Figure 4a and Supplementary Table S6 online). This suggests that the majority of these variants, although individually rare, are benign bystanders, and that any overlap between the disorders has been overestimated.
In the DCM research studies, some genes proposed on the basis of these and other recent studies as among the most common causes of DCM (e.g., MYBPC3, MYH6, and SCN5A15,17,30) in fact showed no excess variation ( Figure 4b and Supplementary Table S7 online).
Reassessment of variants previously reported as pathogenic
We examined the ExAC frequency of variants previously reported to cause HCM, DCM, or ARVC, as catalogued by HGMD (Supplementary Tables S8–S10 online). A substantial number of purported disease-causing variants for HCM (25.2%; 322/1,280), DCM (29.2%; 222/759), and ARVC (34.6%, 167/483) were observed in ExAC. Although presence in ExAC does not preclude pathogenicity, a significant number are present at a frequency incompatible with causation of penetrant cardiomyopathy (6.5% of HCM, 11.9% of DCM, and 13.5% of ARVC variants are present at MAF >1 × 10−4; Supplementary Tables S11 and S12 online). Of HGMD variants that could not be excluded as disease-causing using the Exome Sequencing Project (the largest control data set prior to ExAC) due to an allele count of one, 75% can now be discounted by ExAC refinement. In total, 11.7, 19.6, and 20.1% of individuals in ExAC have reported HCM, DCM, and ARVC variants, respectively; this is far in excess of disease prevalence. Hence, variant prioritization based on HGMD status alone is not advised for cardiomyopathy genes, a fact that is increasingly apparent with larger control data sets.
We present an analysis of data from 7,855 individuals referred for clinical diagnostic testing for inherited cardiomyopathies, along with 60,706 ExAC reference samples. These data exemplify the many challenges of variant interpretation in genetically heterogeneous disorders. We propose that in the absence of a large matched case–control series, the approaches described here, using data from large patient cohorts and broader reference data sets such as ExAC, may be applied to a range of multigenic, multiallelic diseases.
We show that the pathogenicity of disease genes originally identified through family linkage is resoundingly validated, for example, the majority of sarcomere genes in HCM. However, genes implicated in cardiomyopathy through candidate gene studies, including genes on panel tests in routine clinical use, are often not convincingly associated with disease. For example, MYBPC3, MYH6, and SCN5A have all been reported to be major contributors to DCM15,17,30 but show little or no excess burden despite adequate numbers and power; instead, we see that these are in fact genes that have the highest background variation.
We also show that it is crucial not only to distinguish variant classes but also to assess these in light of known disease mechanisms for each gene and disorder. For example, cardiomyopathy-causing variant in most myofilament proteins incorporate into the sarcomere and act as dominant negatives (HCM mutations are activating, whereas DCM mutations decrease myofibrillar function).33 Hence, protein-truncating variants that do not incorporate would not be expected to cause these conditions, and this is borne out in our data. By contrast, MYBPC3 truncation alleles cause HCM through haploinsufficiency, making it unlikely that they could also cause DCM, which we confirm with our findings.
We summarize our analyses of cardiomyopathy genes in two measures, capturing the contribution of each gene to a disease (case excess) and our ability to interpret variation in each gene (etiological fraction (EF)). EF can be interpreted as the proportion of affected carriers in which the variant caused the disease (i.e., the proportion of true positives). EF is based on pooled rare variant frequency data, so it summarizes the average risk across many variants in a gene (some of which will be pathogenic but others will be benign) and will be particularly useful for selecting panels of genes that are informative for discrete phenotypes. Of critical importance, the probability that a novel variant is pathogenic depends on the clinical status of the individual carrying the variant and will be considerably lower in individuals with a remote/unrelated clinical diagnosis. This will be even more problematic with incidental findings during exome or genome sequencing with major implications for the recommendations to return apparently actionable findings.8
Although detailed phenotyping of the clinical cases was not available, we are confident that the clinical diagnoses are robust because the current clinical practice is to test only individuals with a confirmed diagnosis.19,20 The proportion of cases with inherited cardiomyopathy is unknown because evidence of familial disease is not a requirement for testing. The clinical sensitivity (proportion of patients with a pathogenic variant) in our case series was lower than that of previous surveys, which may reflect more restricted testing of stringently selected cases, typically from multiply affected families with severe disease.34,35 However, the cohorts studied are representative of those encountered by clinical diagnostic laboratories, rather than a highly selected subset.
Despite high levels of confidence in interpreting many well-characterized variants (which may give ORs in the hundreds), diagnostic laboratories are understandably cautious when interpreting a variant that has not been seen before. Our analyses demonstrate that for many genes even variants currently reported with variants of uncertain significance show a several-fold excess over the background in ExAC ( Figure 1 ). More refined interpretation of variants in validated genes, for example, leveraging domain information, could increase the diagnostic yield of genetic testing and is likely to lead to much more substantial gains than the expansion of gene panels.
In contrast to the conservative strategy of clinical laboratories, research studies often report large "yields." Some may not adequately control for the background rate of rare variation or may include genes for other conditions; as a result, genes nominated as important contributors to disease have little if any excess variation in cases. Testing of broad gene panels and overly inclusive interpretation of variants may lead to erroneous conclusions about pleiotropic effects of genetic variation14,30 and overestimates of double/compound mutations36 and the population prevalence of the disease.37
Despite the absence of demonstrable excess of rare variation in a gene, specific variants identified in family studies may still be disease-causing. However, if such variants are a small minority of rare variants in cases, then testing will yield more false positives than true positives. For some of the genes that show no excess ( Figure 1 ), the original reports did not include any variant with robust evidence of segregation (i.e., LOD >3), and the possibility exists that the reported disease association is entirely spurious. An argument is often made that variants could be contributing as modifiers.38,39 This remains possible; however, in the absence of any significant overrepresentation in cases, the more parsimonious interpretation is that they are phenotypically silent. We have not tested more common variants (MAF >1 × 10−4) that could be mechanistically informative but are likely to have smaller effects,40 and we have not evaluated individual-level data to assess the impact of coinheritance of variants, which are limitations of the analyses.
A further limitation of this study is that the case and ExAC data were not generated using a single sequencing method; none of the methods used was expected to have 100% sensitivity for variant detection. Although these technical limitations could have marginal effects on estimates of rare variant frequency and OR/EF values, we do not expect them to alter the key conclusions of this study. Because ethnicity data were not available for the Oxford Medical Genetics Laboratory or LMM HCM patients, we were unable to confirm the extent to which the cohorts used in this study were matched by race. However, by studying the aggregate burden of multiple very rare variants, we expect that any confounding effects by individual population-specific variants in cases or ExAC will be limited. Supporting this assumption, an analysis of the LMM DCM cohort comparing findings from all populations with the Caucasian-only subsets revealed that the conclusions are robust (Supplementary Table S13 online).
In conclusion, we have demonstrated that new opportunities for large-scale comparison of rare variation in Mendelian disease genes between patient cohorts and the wider population can identify the genes, regions of genes, and/or classes of variants that can be reliably interpreted in a clinical setting. For validated disease genes, there is clear potential to increase the yield of correctly interpreted, actionable variants. At the same time, problems must be avoided by recognizing that many implicated genes, as well as a significant proportion of variants, may not be robust. As clinical genetic testing moves to ever-larger gene panels and whole-exome and genome sequencing, an understanding of gene and variant pathogenicity will be increasingly important to deliver reliable interpretation.
Data Availability
Web resource Atlas of Cardiac Genetic Variation (http://cardiodb.org/ACGV)
Professor Stuart Cook occasionally consults for Illumina Inc. The other authors declare no conflict of interest.
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The research was supported by the NIHR Oxford Biomedical Research Centre, the NIHR Biomedical Research Unit in Cardiovascular Disease at the Royal Brompton & Harefield NHS Foundation Trust and Imperial College London, the Wellcome Trust, Fondation Leducq, the Tanoto Foundation, the SingHealth Duke-NUS Institute of Precision Medicine (PRISM), the Medical Research Council, the Academy of Medical Sciences, the British Heart Foundation, Arthritis Research UK, and the National Medical Research Council (NMRC) Singapore. K.L.T. is the recipient of a National Institute for Health Research (NIHR) doctoral fellowship (NIHR-HCS-D13-04-006). M.F. and H.C.W. acknowledge support from a Wellcome Trust core award (090532/Z/09/Z) and the BHF Centre of Research Excellence in Oxford (RE/13/1/30181). ExAC was partially supported by U54DK105566 (to D.G.M.) from the National Institutes of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health. We thank the staff at the Oxford Medical Genetics Laboratories (OMGL), Oxford University Hospitals NHS Foundation Trust, for generating and interpreting data used in these analyses.
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Cite this article
Walsh, R., Thomson, K., Ware, J. et al. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med 19, 192–203 (2017). https://doi.org/10.1038/gim.2016.90
Issue Date:
- clinical genetics
- Exome Aggregation Consortium
- inherited cardiomyopathy
- Mendelian genetics
- variation interpretation
Further reading
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PUTRAJAYA: Former prime minister Datuk Seri Najib Razak left the Malaysian Anti-Corruption Commission (MACC) headquarters here after being questioned for more than six hours over allegations of graft related to SRC International.
Najib who exited the building at 4.50pm, stopped to notify reporters that MACC officers had told him that the questioning phase of the investigation has been completed.
"This is the second day of questioning. The session started at 10am ended at 4.30pm with a 40-minute break for rest and Zohor prayers.
"I answered all questions to the best of my ability and MACC officers handled the matter professionally."
"They also told me that questioning is now over," he said.
This is the second round of questioning for Najib over the alleged transfer of RM42 million in his personal bank account.
He and his legal team had earlier pulled up into the MACC headquarters' lobby in a white Toyota Vellfire at 9.45am.
Dressed in a black coat and gray trousers, Najib waved to the gallery of photographers and videographers before being ushered to the investigation room with his lawyers.
In tow were two vehicles, bearing among others his legal team and bodyguards.
Najib was summoned for questioning to facilitate MACC's investigations into the SRC International Sdn Bhd case.
He gave his first statement to the graft busters on Tuesday.
SRC International was a subsidiary of 1Malaysia Development Bhd (1MDB), until it was placed under the Finance Ministry in 2012.
The Prime Minister's Office, in a statement on Monday, had announced the setting up of the 1MDB Investigation Task Force.
Its duties are to conduct a detailed investigation, asset tracing and acquisition as well as facilitate the prosecution of individuals who committed offenses related to the management of 1MDB.
On Tuesday, the US Department of Justice said it would continue to pursue investigations related to 1MDB adding that it was looking forward to working with Malaysian authorities on the matter.
The US filed forfeiture complaints in 2016 and 2017 seeking to recover over USD 1.7 billion in assets traceable to funds allegedly misappropriated from 1MDB.
These complaints alleged that more than USD4.5 billion was diverted from 1MDB and laundered through a web of shell companies and bank accounts located in the United States and elsewhere.--Reports by Hidir Reduan, Veena Babulal, Teoh Pei Ying, Mohd Husni Mohd Noor, Irwan Shafrizan Ismail and Faris Fuad


text:
Instead of doing daily round ups I thought I'd include 3 clusterfucks of information. The first you've probably not read and this is the meaty filling to a review sandwich, think of me like Three Weeks but food like so Three Woks.
Owen Niblock – Calculating Comedy
Ryan's Cellar Bar, 13:15, 3-24
A return to computational based comedy from Niblock. His last show with Gigatron didn't end well so he rebooted and some other computational jokes. A funny look at the construction of comedy with great guests and plus at the end I got to accuse a computer of not being able to run an android game.
Favourite Joke: Had to be the Gigatron's witty retorts at the end.
Nat Luurtsema – Here She Be
The Counting House (Ballroom), 14:45, 3-24
A tale of what happens when you break up with your boyfriend and he happens to be in the three person comedy troupe you're part of. Well you move in with your parents and you begrudge your ex any happiness
Favourite Joke: Reference to Dan Antopolski as Nat and Tom's 30 year old Jewish child they fight over.
Young & Strange – Magic, Illusion & A Hate For Each Other
The Jam House, 18:30, 3-24
The two television featured magicians try to regain their riches by putting on one big 'free' show. A nice opening montage, followed by bickering, great card tricks and a brilliant final illusion then making it snow.
Stuart Ritchie – What's The Point Of Going To School
Banshee Labyrinth – Chamber, 19:50, 14
An informative lecture from the Edinburgh University Psych student, felt very much like a relaxed seminar, questions were forthcoming and it put to bed a few bad headlines. Also came with support for the idea of grammar schools so long as the other children aren't left behind.
Helen Arney + Rob Wells – Domestic Science
The Canon's Gait, 12:10, 3-24
A fun tour through the start of Rob and Helen's relationship. Who knew if you'd ran out of ph paper Sharwoods noodles could do the job for you. A brilliant ending where Helen created a rainbow with the audience to the tune of "Rainbow Connection" by the Muppets.
Rory & Tim – Time To Stand Up
Whistlebinkies, 13:30, 3-24
I've shied away from reviewing showcases as it's unfair to judge people on a small amount of material however the titular sketch duo (the third man didn't think it was time to stand up) descended into madness. A rowdy set of audience members thought they were funnier than the comedians they weren't and they showed their lack of logic by being unable to work out what biological determinism was when Rory clearly explained the concept afterwards. Intelligent humour and when the rude members of the audience left we had a nice parlour game similar to 'Heads Down Thumbs Up" called "Mafia".
Favourite Joke: The Biological Determinism joke was well crafted and deserves an audience who get it.
Wil Hodgson – Kidnapped By Catwoman
The Canon's Gait, 14:25, 3-24
A reprise of last years show with countless comic book references and wandering roads into the past and trips down the chip shop skiving lunch. A nice collection of tales all sewn together with references to strong women, ones that could easily beat you up (not ones that would). I personally loved the references to Batman (Adam West's one) and Wil showed an incredible knowledge of the history of comic books, it was interesting to hear how DC sewed up the market with the Comic's Charter which did the other genres apart from superheroes out of business.
Favourite Joke: The references to Dick Grayson's "Boy Wonder" *wink wink*.
Kate Smurthwaite – News At Kate 2013: World Inaction
The Canon's Gait, 15:40, 3-24
A chat show involving the creator of PBH's Free Fringe, Peter Buckley Hill who answered audience questions including a pretty incisive one about the size of the Free Fringe and if it will plateau from this dashing gentleman at the front (ed. Self deprication is meant to be a British trait). Stand up involving ex-SPAD Alexis Wieroniey an American in London who I'd seen and enjoyed before and Paul B. Edwards.
Favourite Joke: Alexis Wieroniey's nice story about Jack Straw. A nice mental picture there.
Tom Webb – Wedding
Dragonfly, 17:30, 3-24
A nice stand up hour by the versatile comedian (part game show host, part compere, all funnyman). A tale deriving from the fact he is now able to get married in St Paul's Cathedral due to his father's MBE. A trip through the world of dating (and being broken hearted in a long distance relationship) in a packed room (so happy to see this) and all topped off with the saccharine ending of a woman emerging from the crowd and Tom getting married by a Sailor Captain on shore leave. Saccharine but oh so sweet.
Favourite Joke: The end part of the show where Tom wanted to screw over St Paul's by getting married in a non-religious ceremony.
Adam Strauss – The Sordid Sex Life Of The Montane Vole
Ciao Roma, 19:05, 3-24
An altogether different hour from Adam on the same subject and vastly different from the show I saw lat year, this was more straight stand up rather than comic spoken word. Adam spent the hour regaling us with tales of animalia's genitalia and flirting with girls in the audience. It's a hard life. Funny one liners and even the stories had punch, I personally loved this, however I believe it could have been more sordid haha.
Favourite Joke: I love kids, well kids who're related to me, the rest can fuck off.
Kate Smurthwaite – News At Kate 2013: My Professional Opinion
Ciao Roma, 19:20, 3-24
A brilliant hour concentrating on Kate's position as the foremost shout at the nutjobs lady for Radio 5Live, and also This Morning. The This Morning story has to be seen to be believed and includes a tonally perfect impression of Dorries and also Kate screaming into a megaphone.
Favourite Joke: The reversal of Kate and Richard Littlejohn's articles. Amazing that I fell for it but it shows how fluid opinions can be
At this point Tom's show was by far my favourite I've seen, he delivered and carried it right down the aisle and some other wedding pun, Kate's shows are always enjoyable, Adam great and had fun at the others.


text:
Looking for help with making a Tasker Wifi Profile?
Hi, so I'm very new to Tasker and have already posted my question on the Tasker forum at XDA, but did not get the kind of help I was looking for so figured I'd have some luck here.
What I want to do is have Tasker turn off my mobile data when I connect to Wifi and then turn it on again when I disconnect.
Can someone show me step by step how to do this in Tasker?
Thank you!


text:
Oh, it's only the dreamiest collaboration from four of Long Beach's dreamiest ladies, Jenny Stockdale, Alyssandra Nighswonger, Mary McKeever and Tess Shapiro! The Dovelles are steaming down the track after a win at the recent Buskerfest in downtown Long Beach and a recently released EP "Live at 4th St. Vine".[adrotate banner="4″]
The Dovelles
BY: Shea Newkirk - August 28, 2012
Posted in - Artists


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Waving Good-Bye to New Line Cinema
Posted by goldwriting on February 28, 2008
Don't mind him. I've got a pirate copy of Harold and Kumar go to Space right here. It's not even in theaters yet. Now you want some?
Well, another independent studio falls into the gaping maw of the major studios. New Line will officially fold into Warner Brothers and they will compliment their release plates to form a more cohesive schedule. Supposedly the New Line brand will stay on an they will continue to release films that fit the genres they worked in, in essence becoming an indie arm for WB. I can only hope that they will let the studio do what it does best, which is make some really kick ass films, such as: The Lord of the Rings trilogy, The Evil Dead, Critters, most of the Nightmare on Elm Street franchise, Teenage Mutant Ninja Turtles, Pump Up the Volume, My Own Private Idaho, Glengarry Glen Ross, A Few Good Men, Menace II Society, Malice, The Mask, SeVen, Dark City, the Blade trilogy, American History X, Magnolia, the Final Destination trilogy (with another coming in super bloody 3-D), The Cell, Hedwig and the Angry inch, most of the Friday the 13th franchise (including the absolutely hilarious Jason X), Wedding Crashers and Domino. Those are honestly on a sampling of the enjoyment that New Line has brought in their forty years of service to the movie going audience.
So clink your glasses, raise a toast and swallow some popcorn in tribute to a visionary company and let's all hope their name isn't tarnished by big wigs and committee filmmaking.