New Methods for Detecting Lineage-Specific Selection

Siepel, Adam; Pollard, Katherine S.; Haussler, David

doi:10.1007/11732990_17

Cited by 227 publications

(217 citation statements)

References 29 publications

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“…Rare SNVs that cluster within 1 kb were tagged and evaluated for mapping errors. SNVs were annotated for effect on the encoded protein and for conservation by comparison versus sequences of 43 vertebrate species (15) and orthologues in fly and worm (see Methods).…”

Section: Coupling Of Nimblegen Whole-exome Capture To Illumina Sequenmentioning

confidence: 99%

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

Choi

Scholl²,

Ji³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

1,194

876

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Protein coding genes constitute only approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., ''whole exome'') have the potential to contribute to the understanding of rare and common human diseases. Here we report a method for whole-exome sequencing coupling Roche/NimbleGen whole exome arrays to the Illumina DNA sequencing platform. We demonstrate the ability to capture approximately 95% of the targeted coding sequences with high sensitivity and specificity for detection of homozygous and heterozygous variants. We illustrate the utility of this approach by making an unanticipated genetic diagnosis of congenital chloride diarrhea in a patient referred with a suspected diagnosis of Bartter syndrome, a renal salt-wasting disease. The molecular diagnosis was based on the finding of a homozygous missense D652N mutation at a position in SLC26A3 (the known congenital chloride diarrhea locus) that is virtually completely conserved in orthologues and paralogues from invertebrates to humans, and clinical follow-up confirmed the diagnosis. To our knowledge, whole-exome (or genome) sequencing has not previously been used to make a genetic diagnosis. Five additional patients suspected to have Bartter syndrome but who did not have mutations in known genes for this disease had homozygous deleterious mutations in SLC26A3. These results demonstrate the clinical utility of whole-exome sequencing and have implications for disease gene discovery and clinical diagnosis.Bartter syndrome ͉ congenital chloride diarrhea ͉ next-generation sequencing ͉ whole-exome sequencing ͉ personal genomes G enetic variation plays a major role in both Mendelian and non-Mendelian diseases. Among the approximately 2,600 Mendelian diseases that have been solved, the overwhelming majority are caused by rare mutations that affect the function of individual proteins; at individual Mendelian loci, approximately 85% of the disease-causing mutations can typically be found in the coding region or in canonical splice sites (1). For complex traits, genome-wide association studies have identified more than 250 common variants associated with risk alleles that contribute to a wide range of diseases (2, 3). To date, most of these impart small effects on disease risk (e.g., odds ratio of 1.2); moreover, even when extremely large studies have been performed, the vast majority of the genetic contribution to disease risk remain unexplained (4-6). These findings suggest that individually rare variants with relatively large effect may account for a large fraction of this missing trait variance. Indeed, studies addressing this question have documented the presence of individually rare variants with relatively large effect (7,8). Consistent with the Mendelian model, coding variants have proven to be prevalent sources of such rare variants.These considerations motivate implementation of robust approaches to sequencing complete c...

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Section: Coupling Of Nimblegen Whole-exome Capture To Illumina Sequenmentioning

confidence: 99%

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

Choi

Scholl²,

Ji³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

1,194

876

View full text Add to dashboard Cite

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“…To examine whether existing uAUGs were evolutionarily conserved, we analyzed the sequence conservation of the 59 UTRs of uAUG-containing genes using alignments of four yeast genomes (Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, and Saccharomyces kudriavzevii) (http://genome.ucsc.edu). We used the phyloP score (Siepel and Haussler 2006) to evaluate the sequence conservation of each uAUG. Our data showed that in 59 UTRs, AUG was indeed the most conserved among 64 trinucleotides, with an average score of 0.72 versus 0.48 for all 64 trinucleotides in this region (Wilcoxon rank sum test, P < 7.2 3 10 À12 ).…”

Section: Genome Research 1093mentioning

confidence: 99%

A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs

Yen¹,

Adesanya²,

Mitra³

2012

Genome Res.

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Regulatory single-nucleotide polymorphisms (rSNPs) alter gene expression. Common approaches for identifying rSNPs focus on sequence variants in conserved regions; however, it is unknown what fraction of rSNPs is undetectable using this approach. We present a systematic analysis of gene expression variation at the single-nucleotide level in the Saccharomyces cerevisiae GAL1-10 regulatory region. We exhaustively mutated nearly every base and measured the expression of each variant with a sensitive dual reporter assay. We observed an expression change for 7% (43/582) of the bases in this region, most of which (35/43, 81%) reside in conserved positions. The most dramatic changes were caused by variants that produced AUGs upstream of the translation start (uAUGs), and we sought to understand the consequences and molecular mechanisms underlying this class of mutations. A genome-wide analysis showed that genes with uAUGs display significantly lower mRNA and protein levels than genes without uAUGs. To determine the generality of this mechanism, we introduced uAUGs into S. cerevisiae genes and observed significantly reduced expression in 17/21 instances (p < 0.01), suggesting that uAUGs are functional in a wide variety of sequence contexts. Quantification of mRNA and protein levels for uAUG mutants showed that uAUGs affect both transcription and translation. Expression of uAUG mutants under the upf1D strain demonstrated that uAUGs stimulate the nonsense-mediated decay pathway. Our results suggest that uAUGs are potent and widespread regulators of gene expression that act by attenuating both protein and RNA levels.[Supplemental material is available for this article.]Regulatory single-nucleotide polymorphisms (rSNPs) have garnered much attention in recent biomedical studies. Evidence has revealed that rSNPs contribute to human phenotypic variation and can affect disease susceptibility. Furthermore, many disease-associated SNPs identified in genome-wide association studies (GWAS) are noncoding and are most likely regulatory in nature (Hindorff et al. 2009). However, the identification of rSNPs remains challenging. Many researchers have applied computational methods to distinguish functional rSNPs from a large number of neutral noncoding variations, mostly focusing on SNPs in conserved regions. While such approaches have identified many functional regulatory regions, it is not clear whether they can identify the majority of regulatory elements. For example, a recent study analyzed transcription factor binding sites in five different vertebrates and found that most binding events were species-specific. In fact, for one of their transcription factors, CEPBA, only 0.3% of binding sites were conserved across all five species (Schmidt et al. 2010). Transcription factor binding site (TFBS) ''turnover'' and sequence mutation of binding sites are two mechanisms that may explain this high degree of species-specific binding (Odom et al. 2007;Schmidt et al. 2010). These results raise an important question: How sensitive are alignment-...

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“…By definition, these elements are either completely absent or have evolved swiftly in some lineages, significantly reducing the chance that we would identify them as being under constraint . To address the possibility of primate-specific constraint (other patterns of constraint gains and losses are also possible, see Supplemental Material), we used a novel algorithm to detect lineage-specific constrained sequences (Siepel et al 2006). Although our power to detect primate-specific constrained sequences is relatively weak, especially if they are short or have become constrained very recently, we found 94 such sequences (median length 164 bases; range 69-615 bases), some of which are quite striking (Supplemental Figs.…”

Section: Genome Research 767mentioning

confidence: 99%

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Margulies¹,

Cooper²,

Asimenos³

et al. 2007

Genome Res.

Self Cite

191

224

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A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.

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New Methods for Detecting Lineage-Specific Selection

Cited by 227 publications

References 29 publications

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

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