text:
Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing
- Rinki Ratnapriya1Email author and
- Anand Swaroop1Email author
DOI: 10.1186/gm488
© The article is a work of the United States Government; Title 17 U.S.C 105 provides that copyright protection is not available for any work of the United States government in the United States; licensee BioMed Central Ltd. 2013
Published: 11 October 2013
Inherited retinal degenerative diseases (RDDs) display wide variation in their mode of inheritance, underlying genetic defects, age of onset, and phenotypic severity. Molecular mechanisms have not been delineated for many retinal diseases, and treatment options are limited. In most instances, genotype-phenotype correlations have not been elucidated because of extensive clinical and genetic heterogeneity. Next-generation sequencing (NGS) methods, including exome, genome, transcriptome and epigenome sequencing, provide novel avenues towards achieving comprehensive understanding of the genetic architecture of RDDs. Whole-exome sequencing (WES) has already revealed several new RDD genes, whereas RNA-Seq and ChIP-Seq analyses are expected to uncover novel aspects of gene regulation and biological networks that are involved in retinal development, aging and disease. In this review, we focus on the genetic characterization of retinal and macular degeneration using NGS technology and discuss the basic framework for further investigations. We also examine the challenges of NGS application in clinical diagnosis and management.
Genetics of retinal degenerative diseases
The dysfunction or death of retinal photoreceptors is the primary cause of vision loss in the majority of retinal degenerative diseases (RDDs) [7, 8], which are clinically and genetically heterogeneous. In general, loss of photoreceptors in the macular region is termed macular degeneration and results in central vision defects. By contrast, the loss of peripheral vision - for example, in retinitis pigmentosa (RP) - generally starts with rod dysfunction or death that is followed by cone degeneration. RDDs are associated with a diverse spectrum of phenotypes. Some, such as RP, congenital and early-onset retinal degeneration including Leber congenital amaurosis (LCA), and cone-rod dystrophies, are monogenic and non-syndromic. Some syndromic diseases, including Bardet-Biedl syndrome (BBS) and Usher syndrome, exhibit a highly penetrant retinal degeneration phenotype with multiple affected tissues and are also monogenic. Other RDDs, such as age-related macular degeneration (AMD), glaucoma, and diabetic retinopathy, are complex multifactorial entities.
Monogenic RDDs, by definition, are often caused by mutations in a single gene and have a Mendelian pattern of inheritance (dominant, recessive, or X-linked). Genetic-linkage studies in large pedigrees have led to the identification of almost 200 causative genes [9]. Genetic defects in monogenic RDDs are highly penetrant, with little influence of non-genetic factors; nevertheless, clinical severity has often been difficult to correlate to genetic mutation because of variable penetrance, mutations in more than one gene, or modifier variants. The clinical manifestations in complex multifactorial RDDs result from the interplay among multiple susceptibility genes and epigenetic and/or environmental factors; therefore, conventional linkage and positional cloning methods have not been very effective in identifying the underlying genetic cause(s). Candidate gene and genome-wide association studies (GWAS) have been successful in identifying susceptibility loci for complex RDDs. A recent meta-analysis of GWAS discovered at least 19 genes and associated cellular pathways for AMD pathogenesis; these included the complement system (CFH, C2/CFB, C3 and CFI), the high-density lipoprotein pathway (LIPC and CETP), the extracellular or collagen matrix pathway (TIMP3, COL8A1 and COL10A1) and the angiogenesis signaling pathway (VEGFA) [10]. Several loci have also been identified for primary open angle glaucoma [11–13] and diabetic retinopathy [14]. The associated alleles do not, however, specify causality, and further genetic and functional dissection of susceptibility loci will be crucial for understanding their roles in disease pathogenesis.
The discovery of new RDD genes helps in the elucidation of the molecular pathways that underlie retinal development and homeostasis, and in delineating the genetic underpinnings of the degenerative process. Several recent reviews have provided excellent synopses of the genetic and biological features of human RDDs [7, 8, 15–18]. We therefore focus on recent advances in next-generation sequencing (NGS) methods [19] (Boxes 1 and 2) that have provided an unprecedented opportunity for the unbiased discovery of genes and causal variants, and for the comprehensive dissection of the genetic architecture of RDDs. We also highlight the merits and limitations associated with different NGS methods, and present a framework for integrative analyses to elucidate a more complete, multidimensional view of genomic function in retinal health and diseases. Finally, we discuss the progress and challenges in the application of NGS approaches for diagnosis and management of RDDs.
NGS approaches for gene identification in Mendelian RDDs
Extensive genetic and clinical heterogeneity is observed in RDDs that have Mendelian inheritance. Although almost 200 genes have been identified, the genetic defects in many patients are still unknown. NGS offers a rapid, high-throughput and cost-effective approach to identify mutations underlying monogenic disorders.
Whole-exome sequencing
List of novel genes identified in retinal and macular degeneration using next-generation sequencing approaches
Gene symbol
Aberration type
Whole-exome sequencing
Retinitis pigmentosa (RP)
Alu insertion
6-bp deletion
Frame-shift, splice-site
Splice-acceptor, missense
Leber congenital amaurosis (LCA)
Missense and truncation
Congenital stationary night blindness (CSNB)
Missense and truncation
Missense and truncation
Ciliopathy with skeleton abnormality
Missense and truncation
High myopia
Bardet-Biedl syndrome (BBS)
Nephronophthisis with retinal degeneration
ZNF423 and CEP164
Missense, truncation, loss of stop codon
Usher syndrome
Benign fleck retina
Missense and truncation
Cone-rod dystrophy
Knobloch syndrome and retinal dystrophy
Targeted sequencing
RP, cone-rod dystrophy
Usher syndrome
Large insertion
X-linked RP
Intronic mutation
Jobert syndrome
Familial exudative vitreoretinopathy
Candidate exome capture
Retinal- renal ciliopathy
Truncation mutations
cis -Regulatory mapping
Truncation mutation
Candidate exome capture
In a slight variation of WES, candidate exome sequencing captures the selected coding regions that are relevant to a specific genetic trait. Consequently, the examination of a smaller genomic region allows better utilization of resources and the analysis of a larger group of patients. This approach has been useful for ciliopathies, where almost 2,500 genes that are implicated in ciliary function can serve as potential candidates [58]. Candidate exome capture of about 13,000 exons from 828 candidate genes recently identified mutations in the SDCCAG8 gene in patients with retinal-renal ciliopathies [56]. Mutations in a single gene can cause overlapping syndromic phenotypes, and so the candidate exome capture strategy helps in refining genotype-phenotype correlations.
Targeted re-sequencing
Mendelian traits have often been mapped using multi-generational families, narrowing the genomic search space for causal gene identification. Owing to the limited number of meiotic crossing-overs, however, linkage intervals can often span several megabases and include tens or hundreds of transcribed sequences. Intelligent guesses to select and sequence candidate genes can lead to labor-intensive and expensive efforts that often provide limited data on the coding regions of annotated genes. NGS can now be used to capture and sequence large genomic regions of interest, expediting the discovery of causal genes (Table 1).
Whole-genome sequencing
A comparison of next-generation sequencing methodologies
Whole-exome sequencing or candidate exome capture
Customized, economical compared to WGS, manageable data size
Captures genetic variants only in the coding regions of the genome; inefficient hybridization step; high DNA input; susceptible to capture bias
SNP and indel discovery in coding exons; suitable for the identification of causal genes in high-penetrance Mendelian diseases
Targeted re-sequencing
Customized, economical compared to WGS
Genetic variant discovery is limited by array design; high DNA input; inefficient hybridization step; captures only a small proportion of the genome
SNP and indel discovery; suitable for sequencing linkage intervals and genomic regions at or around associated signals
Whole-genome sequencing
Uncovers genome-wide coding and non-coding variants, no capture bias
Expensive; very large dataset; analysis methods are still evolving
Genome-wide SNP, indel and CNV discovery; suitable for rare variant discovery in Mendelian, complex or sporadic traits
Cost-effective method for evaluating known rare variants (MAF of 1 to 5%)
Does not identify novel variants; limited to coding region; limited representation of intronic and regulatory variants
Genome-wide association analysis with rare variants
Array-independent profiling of the transcriptome
High coverage required for the identification of low-copy transcripts; not applicable for the identification of variants that cause loss of protein; limited by tissue- or cell-type availability
Genome-wide expression profiling; alternative transcript identification; non-coding RNA detection; SNP profiling; eQTL analysis
Genome-wide profiling of epigenetic marks (DNA methylation and histone modifications) and cis-regulatory elements
Dependent on the quality of antibody; requires high input; analysis methods still evolving; high coverage needed for accurate profiling
DNA methylation; histone modifications; tissue-specific enhancer profiling
RNA-Seq or transcriptome sequencing
The transcriptome represents a collection of all transcribed sequences (RNAs), both protein-coding and non-coding, in a cell type or particular tissue and at a specific stage of development or age. While microarray technology and methods for serial analysis of gene expression (SAGE) have been valuable, transcriptome profiling using NGS technology (RNA-Seq) is becoming popular because of its ability to survey the transcriptome in a high-throughput and quantitative manner and at low cost [61]. In addition, RNA-Seq has proven useful for annotating protein-coding genes, discovering novel alternatively spliced transcripts and non-coding RNAs (ncRNAs), single nucleotide polymorphism (SNP) profiling, and the detection of gene fusions or rearrangements [62]. DNA-Seq approaches generate a large number of variants and often secondary filtering is required to prioritize the candidate disease genes. Tissue-specific expression profiles therefore offer a valuable first-level screen to identify relevant disease-causing variants (Figure 2).
Profiling of alternative transcripts
In humans, a majority of genes (>90%) undergo alternative splicing to generate tissue-specific and functionally diverse protein isoforms [63]. The role of novel transcripts in diverse pathways and disease causation is slowly being recognized [64, 65]. Retina-specific isoforms of RPGR and BBS3 have been implicated in X-linked RP and BBS, respectively [66, 67]. In addition, mutations in the spliceosome-component genes (PRPF31, PRPF3, and PRPF8) are associated with RP [68]. Thus, retina-specific RNA or transcriptome profiling provides an excellent opportunity to identify novel functionally relevant transcripts. As novel transcripts may be present at low-copy number, RNA CaptureSeq (Box 1) can provide an alternative approach for enrichment [69].
Non-coding RNA
ncRNAs appear to play prominent and diverse roles in normal development, physiology, and disease. Several specific microRNAs (miRNAs) are expressed in the retina (miR-96, miR-182, and miR-183) [70, 71] and RPE (miR-204/211) [72]. Long antisense (non-coding) transcripts have been associated with eight transcription factors that are involved in eye development [73], and two ncRNAs, TUG1[74] and Six3OS[75], have been linked to retinal differentiation. Inactivation of DICER1, an RNase III endonuclease that is essential for the production and function of mature miRNAs, has been implicated in retinal degeneration [76], and Alu RNA toxicity has been suggested to a play a role in AMD [77]. Thus, further exploration of ncRNAs seems essential, and RNA-Seq offers a starting point for the identification of novel ncRNAs in development and disease.
SNP profiling
Genetic variations within the transcribed (coding or non-coding) regions of the genome can alter the expression or function of the encoded sequence. Therefore, RNA-Seq can provide profiles of genetic variants in both the quasi-complete set of transcribed genes (mRNAs) and ncRNAs in a cost-effective manner and without the need for target-probe hybridization, a necessary but inefficient step in capture-based methods. However, RNA-Seq should be applied with caution, as it is possible to miss variants that result in the loss of a gene product.
ChIP-Seq-based approaches
The genomic location and function of regulatory elements contributes significantly to the development of human diseases. Chromatin immunoprecipitation followed by NGS (ChIP-Seq) can be used to profile cis-regulatory elements (CREs) (Box 1), which include transcription factor binding sites clustered within promoters, enhancers and silencers [78]. ChIP-Seq has been employed to generate genome-wide maps of CREs for two key photoreceptor-specific transcription factors, CRX[79] and NRL[80]. In addition, these data have permitted the prioritization of disease-associated genes or variants for further study. Not surprisingly, several CRX and NRL target genes are associated with RDDs [79, 80], and recently, CRX ChIP-Seq data were used to filter the candidates to identify mutations in MAK (encoding a regulator of ciliary length) as a cause of autosomal recessive RP [57].
ChIP-Seq can also be employed for genome-wide profiling of epigenetic modifications, such as DNA methylation and covalent modifications of histones [81]. Epigenetic variations can influence gene expression and developmental programming [82, 83]. Evidence suggests the involvement of epigenetic mechanism in RDDs; but such modifications are more likely to be associated with complex disorders, such as AMD [84], glaucoma and diabetic retinopathy. Epigenetic profiling of retina, RPE and other eye tissues or cells, in combination with gene profiling, should provide valuable insights into disease mechanisms. The Encyclopedia of DNA Elements (ENCODE) project has systematically integrated gene expression data with information on regulatory elements, transcription factor binding, and epigenetic modifications for as much as 80% of the genome [85]. Expression profiles and other data relevant to retinal and macular diseases have not, however, been incorporated as yet.
NGS approaches for complex traits
The identification of the genetic susceptibility variants underlying complex multifactorial disorders requires extensive efforts including large patient cohorts and cumbersome analytical tools. GWAS have been successful in uncovering associated loci for numerous diseases, but such studies only examine common (tagging) variants in populations and additional investigations are necessary to identify causality. In this section, we provide an overview of the possible applications of NGS, with an emphasis on the study design for complex diseases.
GWAS and meta-analysis
Rare variant identification
The hypothesis that rare variants influencing a complex trait should co-localize with associated common alleles has accelerated targeted re-sequencing of the GWAS loci [90]. Such studies have led to the identification of rare coding variants, R1210C in CFH[49] and G119R in CFI[12], that are associated with AMD. WES studies are also being performed to test the association of rare coding variants with a complex phenotype [91, 92]. However, such studies require a large sample size to achieve the statistical power necessary to detect a significant association that can then justify multiple testing. In the absence of such a dataset, extreme phenotype study design, in which samples from both ends of the phenotype distribution are analyzed, can serve as a suitable alternative (Figure 3) [93]. In addition, inherited macular dystrophies share common clinical characteristics with AMD, and occasionally genes identified in heritable forms, such as TIMP3[94] and ABCA4[95], have been associated with AMD [88, 96]. Thus, WES and WGS in families with macular dystrophies (and occasionally in available AMD families) can uncover rare variants that might contribute to disease pathophysiology.
Copy number variations
Large DNA stretches (>1 kb) that exhibit variable copy number when compared to the reference genome contribute significantly to population dynamics and evolution. Comparative genomic hybridization (CGH) arrays and SNP arrays have been commonly used to detect copy number variations (CNVs) that are implicated in neurodevelopmental (autism, schizophrenia, and intellectual disability) and immune-related diseases (Crohn's disease, psoriasis, HIV/AIDS, rheumatoid arthritis, and type I diabetes) [97]. The role of CNVs is under investigation in AMD [98–100]. An 84-kb deletion spanning CFHR1 and CFHR3 has been associated with protection against the development of AMD [101–103]. A recent GWAS has identified CNVs at NPHP1 and EFEMP1 as potential candidates for AMD association [100]. CNVs in additional genes, such as CCR3, CFH, CX3CR1, ERCC6, HTRA1, VEGF, GSTM1, and GSTT1, have also been associated with AMD [104]. Nevertheless, a complete spectrum of CNVs in complex diseases (including AMD) has not been realized yet because of the limited resolution of current methods. NGS-based CNV detection utilizes high-coverage WGS data for unbiased detection of CNVs at much higher resolution than has been available to date, providing information about CNV breakpoints and the location of copy number gains [105, 106]. Nevertheless, methodologies for CNV detection using NGS lack well-defined workflows, protocols, and quality-control measures, imposing substantial computational and bioinformatic challenges [107]. In addition, databases for human structural variation are limited and contain inadequate information on most breakpoints. A validated pipeline for structural variation analysis using NGS data is highly desirable for utilizing the full potential of CNVs for complex trait analysis.
A common-variant-based GWAS approach has not explained the complete genetic variance observed in complex traits. Missing heritability might be explained by rare to low frequency variants (minor allele frequency (MAF) of 1 to 5%) [90, 108, 109]. NGS studies, such as the 1,000 Genomes Project [110] and the NHLBI Exome Sequencing Project [111], have identified a large number of such variants, leading to a second-generation genotyping array for testing the association of rare variants in complex traits [112]. Ideally, all common GWAS variants that are associated with distinct phenotypes can be included in such exome-chips. Although any regulatory or novel rare variant is not identified by this approach in RDDs, exome chips offer an economical and rapid platform that can be used to test the hypothesis that certain rare variants are causal alleles in common diseases. Such studies are currently in progress as part of a large AMD consortium and should identify novel variants and genes in the near future.
Expression quantitative trait loci analysis
A vast majority of disease-associated SNPs identified in GWAS are reportedly located in non-coding regions of the genome, and their functional role in causing the disease is generally not understood. Arguably, such variants might regulate gene expression and act as expression quantitative trait loci (eQTL) [113]. Combined analysis of genotyping with RNA-Seq data provides a unique opportunity to correlate genetic variations and expression level at disease-associated loci [114]. Expression profiling is more relevant, however, when implemented in disease-affected tissues or cell types. Although little has been reported on the importance of eQTLs in RDDs, the integration of data on modifier and susceptibility variants with the NGS expression data would facilitate the elucidation of complex regulatory networks that can provide insights into novel intervention strategies.
Making sense of the vast amount of NGS data for disease gene identification
The identification of relevant candidate disease-causing variants from NGS data requires filtering strategies that depend on multiple factors, such as the availability of well-phenotyped patient cohorts, knowledge of the mode of inheritance, and large sample sizes. Computational tools that can predict the impact of a variant on protein function can assist in segregating the deleterious variants from neutral ones [115]. A general guideline for candidate variant identification is provided for Mendelian (Figure 2) and complex RDDs (Figure 3), but each biological question might require a unique approach. For example, homozygosity and linkage data can complement WES or targeted sequencing in Mendelian RDDs [30, 31, 45–47]. Similarly, the integration of GWAS data with rare variant, eQTL or pathway-based analyses can yield meaningful results for complex traits such as AMD. Ultimately, validation of genetic causality would require additional investigations using in vitro assays and/or model organisms.
NGS in diagnostics and disease management for RDDs
Over 200 genes have been implicated in RDDs, offering an opportunity to clarify etiology, provide prognosis, and calculate associated risk(s). Nevertheless, molecular diagnosis and counseling are complicated by genetic heterogeneity and extensive phenotypic variability. Mutations in the same gene can cause different phenotypes and similar clinical findings can result from mutations in different genes. For example, RPGR and RP2 are primary causative genes in X-linked RP, but recent studies have reported the prevalence of RP2 and RPGR mutations even in simplex retinal degeneration in males [116] and in pedigrees with 'apparent' autosomal dominant inheritance of RP [117]. Thus, the boundaries of distinct clinical entities can be blurred, demanding more comprehensive methods of molecular evaluation [118].
Customized arrays have been developed for screening patients with RP [119, 120] and other retinal dystrophies [121, 122]. The National Eye Institute has established the National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE®), which offers molecular diagnosis as a service [123]. The eyeGENE® network currently includes Clinical Laboratory Improvement Amendments (CLIA)-certified diagnostic laboratory partners; over 270 registered clinical organizations with 500 registered users from around the United States and Canada have analyzed over 4,400 samples. eyeGENE® is also working towards setting up high-throughput genotyping and sequencing technologies for improved clinical sequencing. These efforts, however, need continuous validation of reliability, robustness and reproducibility of the technology being employed. Implementation of NGS hardware requires substantial in-house infrastructure and a standardized guideline for NGS protocols. Issues related to the ownership and confidentiality of genomic data and the handling of incidental or secondary findings (Box 1) must also be addressed before NGS technology moves into routine clinical practice.
Understanding the biology of disease
The extreme phenotypic variability in RDDs can be attributed to allelic heterogeneity, modifier loci, and epigenetic and environmental factors, or a combination of these. A modifier gene is predicted to alter the phenotypic outcome of a given genotype by interacting with the primary disease gene or by functioning in the same or a related biological pathway, affecting penetrance, expressivity and pleiotropy [124, 125]. A few examples are warranted. Digenic inheritance has been reported for mutations in ROM1 and peripherin/RDS resulting in RP [126] and for ROM1 and ABCA4 mutations in macular dystrophy [127]. CNOT3 can modify the phenotype of a PRPF31 mutation in RP [128]. The potential involvement of mutations in more than one causative gene has also been described in LCA [129]. Phenotypic differences in ciliopathies are also attributed to modifiers [130, 131]. For example, a common allele in RPGRIP1L, Ala229Thr, is reported to be a modifier of retinal degeneration in ciliopathy patients [132]. AHI1 seems to act as a modifier of CEP290[133] and NPHP1[134], and PDZD7 can modify the phenotype in Usher syndrome patients who have a homozygous USH2A mutation [135]. The search for modifiers has, however, been limited because of their non-Mendelian segregation and restricted exploration within known RDD genes, and because of the abundant normal genetic variations in humans. NGS approaches offer an expanded platform for genome-wide evaluation of modifier variants that would permit a better understanding of phenotypic variability and progression in RDDs.
Mouse models have provided valuable insights into RDD pathogenesis, but complex interactions among retinopathy proteins and additional variants can exacerbate or ameliorate the disease phenotypes. For example, mice that had a combination of Cep290 and Mkks disease alleles had better sensory functions than those with either mutation alone [136]. The development of therapeutic strategies would therefore require a comprehensive understanding of RDD gene interaction networks and cellular pathways. NGS technology should expedite the integration of genetic variants in relevant RDDs and modifier genes with retinal transcriptome and epigenetic profiles.
Conclusions, challenges and future prospects
It is an exciting time in the genetic analysis of RDDs as NGS has led to unprecedented access to various genome-wide datasets. NGS has proven successful in identifying the genetic cause of monogenic RDDs in many patients and families and offers great promise for the genetic dissection of complex RDDs. With the generation and analysis of NGS data becoming more accessible and affordable, a comprehensive catalog of variants for most (if not all) vision-related traits seems a viable prospect. Whole-transcriptome and epigenome analysis in retinal tissues would greatly facilitate the elucidation of important pathways or networks underlying development and disease. In this review, we have highlighted the challenges and the opportunities in applying NGS for gene discovery and clinical diagnosis of RDDs. A major goal lies ahead in developing a unified framework for identifying all disease-relevant variants and genes. Methods for downstream bioinformatic analyses are still evolving and represent a major bottleneck in NGS applications. There is significant room for improvement in mapping and variant-calling methods, especially for small insertions or deletions and CNVs. Better tools are required for combining information from across studies that have used different sequencing platforms or even distinct methods of data analysis. As each kind of NGS data has its own merits, integrated and multidimensional analyses of biological systems with relevant clinical information records would be valuable for intervention and personalized medicine.
Box 1. Glossary
Next-generation sequencing (NGS): also known as massively parallel sequencing or high-throughput sequencing; these recent technologies allow parallel sequencing of multiple samples and produce millions of sequence reads concurrently, thereby reducing the sequencing costs and time considerably.
Mendelian disease: also called monogenic disease; results from single genetic defect(s) that are passed on to the next generation in a Mendelian inheritance pattern (dominant, recessive, or X-linked).
Complex disease: a multifactorial disease that does not exhibit a simple Mendelian inheritance pattern and is caused by complex interplay among genetic, epigenetic and environmental factors.
Simplex case: also known as sporadic cases; those in which only a single individual has a clinical diagnosis and no relatives are affected.
Whole-genome sequencing (WGS): sequencing of the complete DNA of an organism's genome.
Whole-exome sequencing (WES): capture and sequencing of the coding exons of all genes, comprising roughly 1 to 2% of the genome.
Targeted re-sequencing: sequencing of a defined (targeted) region of the genome; helpful in identifying disease variant(s) when a linkage region has been established.
Transcriptome: the complete set of coding and non-coding transcripts (RNAs) expressed in a specific cell type, tissue or organism.
RNA-Seq: sequencing of transcriptome using NGS; RNA-Seq includes only the transcribed sequences of the genome.
RNA CaptureSeq: use of tiling arrays to capture and sequence selected portions of the transcriptome.
Chromatin immunoprecipitation (ChIP): a method for investigating the genomic DNA region(s) that are interacting with a protein in vivo, by capturing the DNA that is bound to a specific antibody.
ChIP-Seq: combines ChIP with NGS to generate a genome-wide map of DNA-binding proteins; can be used to identify genome-wide epigenetic marks on histones.
cis -Regulatory element (CRE): DNA sequence in or near a gene (in cis) containing binding sites for transcription regulatory proteins that control the spatiotemporal expression of the target gene.
Single-end sequencing: sequencing of a DNA molecule only from one end; as NGS reads can be small, single-end sequencing might not be efficient in mapping low complexity and repetitive regions of the genome.
Paired-end sequencing: sequencing of a DNA molecule from both ends, resulting in a superior alignment across the genome.
Mapping sequence assembly: mapping of NGS reads to a reference genome.
De novo assembly: a method of generating large assemblies of NGS reads in the absence of a reference genome.
Single nucleotide polymorphisms (SNPs): genetic variations that alter a single nucleotide in the genome.
Insertion-deletion variation (indel): any sequence change that leads to the addition or removal of one or more nucleotides compared to the reference genome.
eQTL analysis: analysis of genomic loci that have statistically significant correlation between genotype and gene expression levels, and thus regulate gene expression levels.
Copy number variation (CNV): a segment of DNA (>1 kb) that is present at a variable copy number compared to the reference genome, altering the diploid status at a particular locus.
Deleterious variant: a DNA change that lowers the fitness of the gene by altering the expression or function of the encoded protein or RNA and remains under the selection of various strengths.
Neutral variant: a variant that does not alter the function of a gene or confer any influence on the fitness of a gene.
Conserved variant (or conserved residue): a DNA nucleotide or amino acid residue that shares identity among closely related species.
Private variant: a genetic variant that is confined to a single individual or a family.
Incidental or secondary findings: refers to the identification of any genetic finding that has health or reproductive relevance for the patient, but was not obtained as a part of the original goals of the study.
Box 2. Next-generation sequencing methods
Next-generation sequencing: also known as massively parallel sequencing or high-throughput sequencing, this process enables the sequencing of a large number of DNA sequences in a single reaction; NGS has revolutionized the genomics field by producing fast, inexpensive and accurate sequencing data.
Platforms: several NGS platforms are commercially available, including Roche/454, Illumina/Solexa, ABI SOLiD, Life/APG, Helicos BioSciences and Pacific Biosciences; Illumina is a widely used platform because it provides large throughput at low cost.
Template preparation: starting material (genomic DNA, cDNA or immuno-precipitated DNA) is sheered to small-size fragments of 30 to 400 base pairs and ligated to a universal adapter. DNA can then be amplified using emulsion PCR or bridging amplification, followed by sequencing, or in the case of single molecule templates, sequenced directly.
Sequencing reaction: NGS chemistry methods (cyclic reversible termination, sequencing by ligation, pyrosequencing and real-time sequencing) vary among different platforms; sequencing by synthesis (SBS) is a commonly used approach that includes the use of DNA polymerase or DNA ligase for stepwise nucleotide addition.
Output: high throughput is a key feature of NGS protocols, with a single run producing several gigabases (Gb) of sequence data. Output varies among platforms; for example, Illumina HiSeq 2000 produces 95 to 600 Gb and SoLiD/ABI 5500 produces 90 to 300 Gb in a single run.
Assembly and mapping: once sequencing is accomplished, the initial analysis of base calling is performed by proprietary software on the sequencing platform, followed by aligning the data to a known reference genome if available or by de novo assembly; short read lengths can make mapping in the repetitive regions challenging.
Analysis: downstream analysis varies depending on the biological question; DNA-Seq data are subjected to variant and CNV detection, whereas RNA-Seq data are used to characterize the transcriptome and ChIP-Seq is used for large-scale analysis of chromatin features.
Age-related macular degeneration
Bardet-Biedl syndrome
- ChIP:
Chromatin immunoprecipitation
Copy number variation
cis-regulatory element
- eQTL:
Expression quantitative trait loci
Genome-wide association studies
Long wave-length
Leber congenital amaurosis
Medium wave-length
Minor allele frequency
- miRNA:
- ncRNA:
Non-coding RNAs
Next-generation sequencing
Retinal degenerative diseases
Retinitis pigmentosa
Retinal pigment epithelium
Short wave-length
Single nucleotide polymorphism
Whole-exome sequencing
Whole-genome sequencing.
We thank Dr Emily Chew (National Eye Institute, National Institutes of Health, Bethesda, MD) for providing the fundus photograph of the human retina. This work is supported by the Intramural Research Program of the National Eye Institute.
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This article is published under license to BioMed Central Ltd.


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Need PHP Help!
- Status Closed
- Budget $30 - $250 USD
- Total Bids 10
Project Description
Project Description:
This project requires someone with extensive knowledge in PHP and MySQL. We have a website ([url removed, login to view]) which is live at this time. When you visit the site you will see that the homepage loads a map of the state of West Virginia. Users are then able to click on a specific region in the map and are taken to the classifieds that are listed in that area. Our main goal of this website is to generate enough website traffic in order to start selling advertisements to businesses and organizations in the specific regions of the state. Myself and my business partner have set up the website and got it this far; however, we are stuck when it comes to modifying the website even further to suit what we are trying to acheive. Please review and make certain that you will be able to acheive all the tasks below before bidding on this project.
1) Make each regional page display a list of categories. For instance, go to ([url removed, login to view]) we want the categories to only show the classifieds within that region, but we want the whole category list to appear even if there are no items present like how it shows on classifiedads.com. We would also like the icons to show on each category heading as well.
2) On each region page present a "carousel" (like displayed on [url removed, login to view] ) of premium ads that users can pay to have the additional exposure. We would like this displayed above the categories on the top of the page, but below a paid slider banner for paid commercial space.
3) The main search bar on our homepage should search all items in the entire state. Conversely, each region should have their own search bar that only searches within that specific region.
4) Create a place on the Admin page so we can administer commercials ads on each regional page and category pages. For example, if we have a car dealership that would like to commercially advertise under our automobile listings – we want to be able to assign their ad to that specific category and region.
5) Add field for seller phone number to display with ad. Optional for seller to display it.
6) When mouse over region on main state page. Display the region in bold with list of counties in small font. This will help users learn their region names.
7) Each category per region will need space down the right column for commercial ads- example if a regional car dealer wants to buy an ad they can buy an ad at the regional category of cars level. These would be the lower price commercial ad spaces. Each category should have such a commercial space on right column.
8) Add the US $ signs before the price. And fix the comma problem for when sellers post the dollar amount. Right now when users add an item that is over $1,000 and adds a comma into the price. It truncates the number and sees the comma as a period.
This looks like a bunch of work on paper, but should be relatively simple to someone who understands and works in PHP. Thank you for your interest in this project and we hope to be working with you soon.Get free quotes for a project like this
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- Author: Unknown author
- Format:Hardback
- Publisher:Canterbury Press Norwich
- Published:June 2000
Sorry, there are currently no sellers for this product.
Product description
- Total Pages: 1400
- Genre: Christian hymnals
- Secondary Genre: Anglican & Episcopalian Churches, Church of England
Since it was first introduced in the Summer of 2000, Common Praise the new Hymns Ancient & Modern has sold over one hundred thousand copies, and been adopted by parishes in every diocese in England and Wales including eight English cathedrals and in five of the seven dioceses in Scotland. It is also used in numerous schools, colleges, hospitals, residential homes, retreat houses, religious communities, crematoria, missions and military garrison chapels.


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Day 22, Penang, Malaysia
Trip Start Mar 12, 2013
74Trip End Jun 02, 2013
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What I did
Chinese temple, Burmese Temple, History Museum
Woke up to pouring rain. Visibility not much.
Our tour started around 10a and we hoped that the weather would improve, but it did not. I took the umbrellas and my rain jacket. Rich took no jacket. Can you see where I am going with this?
We toured some temples, museum, etc. The coach was not that close to the entrances so we had to walk through puddles and the rain. It was a good thing the weather was on the warm side.
We did have a nice tea at the E & O Hotel. We had chicken satay, curried puffs, a tray full of tiny sweets and tea/coffee. I said to Rich, be sure and grab your umbrella, he, of course, said no. When it was time to leave, the rain was pouring buckets. Guess who got wet and guess who stayed dried? To make matters worse, the bus was below freezing. I felt like we were in a cold storage locker. We still had one more stop in the pouring rain. We decided to forgo that last stop. It was to walk out on a jetty and look at the non-view.
By the time we got back to the ship the rain had let up a bit, but still no clearing in sight. We had a light lunch at Le Veranda and ice cream by the pool deck.
Triva was a bust for us today. We just did not know many answers. How many eye lids does a bird have? Who knows...... It was all rubbish questions as far as we were concerned. But, we have a great time with our friends.
Tonight we dined alone in CR and it was a nice evening. I got to watch the sun set and took many pictures. Yes, the sun decided to come out as we started sailing. Go figure.
We have an 8 hour excursion tomorrow, back in my favorite country, Thailand. Cannot wait to see Phuket.
We would love to come back to Malaysia and just hang out and see everything there is to see. Another item in our bucket. I feel we are only touching the surface of these great countries and we want to see more and more.
Until next time...


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Casa del Golf La Maroma offers accommodation in Osma, 41 km from Salta and 22 km from La Merced. The property is 48 km from San Lorenzo and free private parking is offered. The nearest airport is Martin Miguel de Güemes International Airport, 34 km from the property. more


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I was sent this by someone who can barely turn the computer on.
http://www.pioneerplanet.com/living/hom_docs/017807.htm >>
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That's all I found too, and it's just the captions under the photos. It seems
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Approved for 1.0 CLE credit hour
Approved for 1.0 CLE credit hour.
Dennis Stanchik, Dennis J. Stanchik P.A., Olathe
This program is the part two continuation of the January 29, 2014 presentation of Interpreting the Revised Kansas Code for Care of Children— Where are the Pitfalls? These two phone CLEs can be viewed independently of one another and do not have to be viewed together in order to receive full credit.
The presentation will focus on three areas of the RKCCC that present potential problems to the practitioner. Specifically, the presentation will focus on: (1) K.S.A. 38-2272(d) and the possible unintended consequences when the court retains jurisdiction after appointing a permanent custodian; (2) whether K.S.A. 38-2286 provides any effective relief for a grandparent who has not been appointed as custodian or designated as placement for a grandchild; and, (3) whether the line of cases interpreting the provisions of K.S.A. 38-2273(a) have established a two pronged test for determining whether a particular order entered in a case governed by the RKCCC may be appealed. If time permits, the presentation will also discuss appellate opinions interpreting the RKCCC published in 2013.
For more information, please view the brochure.
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2/17/2017Supreme Court to conduct special evening session at Southwestern College
12/16/2016Kansas Bar Foundation awards $70,000 in grants and scholarships
12/8/2016Judge Karen Arnold-Burger selected as chief judge of the Kansas Court of Appeals
2/7/2017 » 3/23/2017Mesa CLE Webinars-February and March
3/1/2017Neosho County Bar Association Meeting
3/2/2017KBA Webinar: FLSA White Collar Exemptions
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Chocolat: A Novel
Penguin Books, 2000 - Fiction - 306 pages
Illuminating Peter Mayle's South of France with a touch of Laura Esquivel's magic realism, Chocolat is a timeless novel of a straitlaced village's awakening to joy and sensuality. In tiny Lansquenet, where nothing much has changed in a hundred years, beautiful newcomer Vianne Rocher and her exquisite chocolate shop arrive and instantly begin to play havoc with Lenten vows. Each box of luscious bonbons comes with a free gift - Vianne's uncanny perception of its buyer's private discontents and a clever, caring cure for them. Is she a witch? Soon the parish no longer cares, as it abandons itself to temptation, happiness, and a dramatic face-off between Easter solemnity and the pagan gaiety of a chocolate festival. Chocolat's every page offers a description of chocolate to melt in the mouths of chocoholics, francophiles, armchair gourmets, cookbook readers, and lovers of passion everywhere. It's a must for anyone who craves an escapist read, and is a bewitching gift for any holiday.
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LibraryThing ReviewUser Review - SueinCyprus - LibraryThing
This book was pleasant, well-written, and a bit different from most modern books - but having finished it, I'm not sure why so many people rave over it. The story is about Vianne Rocher, a single ... Read full review
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LibraryThing ReviewUser Review - BookConcierge - LibraryThing
This book reminds me of The Mistress of Spices (which, in turn, reminded me of Like Water for Chocolate). Viane is so calm in the face of other's pettiness, so confident. And yet, haunted by her late ... Read full review


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We hope everyone enjoyed their season.
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[Date Index] [Thread Index] [Author Index]
Contexts and Naming of Things
I have the following code which does not work as I had hoped. I first declare a function in a package... BeginPackage["HSSV`cavity`"] foo::usage = "now is the time..." Begin["`Private`"] bar; nebbish; foo[x_, y_] := 1 /; y === bar; foo[x_, y_] := 2 /; y === nebbish; End[] EndPackage[] And then try to run the following simple commands... foo[1, bar] foo[1, cavity`bar] foo[1, HSSV`cavity`bar] I had thought that the first one would have given me the correct answer, as it works OK when I do not embed the function definition in a package. The others were desperate second efforts that also failed. What am I missing here?


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The Price of Peace
Just War in the Twenty-first Century
Edited by Charles Reed David Ryall
Foreword by Dr. Rowan Williams
Format: Hardback
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Price of Peace by Charles Reed
Book DescriptionLively political and public debates on war and morality have been a feature of the post-Cold War world. The Price of Peace argues that a re-examination of the just war tradition is therefore required. The authors suggest that despite fluctuations and transformations in international politics, the just war tradition continues to be relevant. However they argue that it needs to be reworked to respond to the new challenges to international security represented by the end of the Cold War and the impact of terrorism. With an interdisciplinary and transatlantic approach, this volume provides a dialogue between theological, political, military and public actors. By articulating what a reconstituted just war tradition might mean in practice, it also aims to assist policy-makers and citizens in dealing with the ethical dilemmas of war.
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Book DetailsISBN: 9780521860512
(228mm x 152mm x 24mm)
Pages: 360
Imprint: Cambridge University Press
Publisher: Cambridge University Press
Publish Date: 15-Feb-2007
Country of Publication: United Kingdom
Other Editions...
Books By Author Charles Reed
Memoirs of the Life and Philanthropic Labours of Andrew Reed, D.D., Paperback (November 2011)
The biography of the committed Congregational minister and energetic London philanthropist Andrew Reed (1787-1862), first published in 1863.
Price of Peace, Paperback (February 2007)» View all books by Charles Reed
A re-examination of the Just War tradition in the context of the twenty-first century.
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Author Biography - Charles Reed
Charles Reed is the International Policy Advisor to the Church of England's Mission and Public Affairs Unit. He is a specialist on the ethics of war and peace and is the author of Just War? (2004). David Ryall is the Assistant General Secretary at the Catholic Bishops' Conference of England and Wales. He has taught politics at the University of Wales and has published articles in International Relations, Third World Quarterly and The World Today.
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LCDs definitely provide depth and texture. The impact of the LCDs is debatable depending on how impact is defined. I personally perceive a sense of impact from the LCDs. However it is not in the same sense that I perceive impact from the 2Ks. The 2Ks provide more of a sense of physical impact like a subwoofer against your face, whereas the LCDs impact is less physical, but more sonic impact. It is kind of like the perception of impact from the 2Ks comes from the cans, whereas the perception of impact of the LCDs comes from the recording (i.e. how the instruments were played or the sounds generated).
I'd say both provide a good sense of impact, but of a different nature.
I think I know what you mean. I have the D5000's and just got an LCD 2 (have yet to really use them fully amped just yet since I just moved) but I know what you're saying with the physical impact of the denons and how they literally will vibrate on your ears like mini subwoofers lol. My old headphones were beyerdynamic dt990's 32 ohm version which had more of the sonic type bass, although I still found them to be a bit bass shy like neither a true sonic impact or physical impact just bass tone really. While sonic impact is like feeling the bass inside your head or ears rather than ON your ears with the literal vibration of the ear cups themselves. Sometimes I dont like when my denons vibrate like that when I have them turned up and have some EDM playing because it starts getting a little annoying physically and makes me feel like I should be hearing that sonically not just physically, since they dont seem to have as much sonic impact as they do physical impact (if we are going with the definitions of sonic vs. physical I laid out). So yea, excited to break in the LCD's and I got a Burson Soloist SL for them too.