Transcriptome Sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants

Recent and rapid human population growth has led to an excess of rare genetic variants that are expected to contribute to an individual’s genetic burden of disease risk. To date, much of the focus has been on rare protein-coding variants, for which potential impact can be estimated from the genetic code, but determining the impact of rare noncoding variants has been more challenging. To improve our understanding of such variants, we combined high-quality genome sequencing and RNA sequencing data from a 17-individual, three-generation family to contrast expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) within this family to eQTLs and sQTLs within a population sample. Using this design, we found that eQTLs and sQTLs with large effects in the family were enriched with rare regulatory and splicing variants (minor allele frequency < 0.01). They were also more likely to influence essential genes and genes involved in complex disease. In addition, we tested the capacity of diverse noncoding annotation to predict the impact of rare noncoding variants. We found that distance to the transcription start site, evolutionary constraint, and epigenetic annotation were considerably more informative for predicting the impact of rare variants than for predicting the impact of common variants. These results highlight that rare noncoding variants are important contributors to individual gene-expression profiles and further demonstrate a significant capability for genomic annotation to predict the impact of rare noncoding variants.

[1]  Eurie L. Hong,et al.  Annotation of functional variation in personal genomes using RegulomeDB , 2012, Genome research.

[2]  Xin Li,et al.  Efficient identification of identical-by-descent status in pedigrees with many untyped individuals , 2010, Bioinform..

[3]  T. Borodina,et al.  Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.

[4]  S. Gabriel,et al.  Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants , 2012, Nature.

[5]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[6]  Claudio J. Verzilli,et al.  An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People , 2012, Science.

[7]  J. Pritchard,et al.  The deleterious mutation load is insensitive to recent population history , 2013, Nature Genetics.

[8]  D. Koller,et al.  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals , 2013, Genome research.

[9]  A. Clark,et al.  Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants , 2012, Science.

[10]  Gonçalo R. Abecasis,et al.  Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability , 2011, PLoS genetics.

[11]  Jacob A. Tennessen,et al.  Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes , 2012, Science.

[12]  Jacek Majewski,et al.  Genome-wide analysis of transcript isoform variation in humans , 2008, Nature Genetics.

[13]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[14]  J. Lupski,et al.  Clan Genomics and the Complex Architecture of Human Disease , 2011, Cell.

[15]  Isabelle Cleynen,et al.  Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease , 2011, Nature Genetics.

[16]  Joseph K. Pickrell,et al.  A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes , 2012, Science.

[17]  Matthew Stephens,et al.  Dissecting the regulatory architecture of gene expression QTLs , 2012, Genome Biology.

[18]  S. Batzoglou,et al.  Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.

[19]  Manolis Kellis,et al.  HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants , 2011, Nucleic Acids Res..

[20]  Greg Gibson,et al.  Rare and common variants: twenty arguments , 2012, Nature Reviews Genetics.

[21]  Sivakumar Gowrisankar,et al.  A rare penetrant mutation in CFH confers high risk of age-related macular degeneration , 2011, Nature Genetics.

[22]  Gary D. Bader,et al.  The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function , 2010, Nucleic Acids Res..

[23]  R. Durbin,et al.  Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses , 2012, Nature Protocols.

[24]  E. Dermitzakis,et al.  Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes , 2011, PLoS genetics.

[25]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[26]  R. Guigó,et al.  Transcriptome genetics using second generation sequencing in a Caucasian population , 2010, Nature.

[27]  Taylor J. Maxwell,et al.  Deep resequencing reveals excess rare recent variants consistent with explosive population growth , 2010, Nature communications.

[28]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[29]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[30]  A. Pandey,et al.  Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. , 2012, Molecular bioSystems.

[31]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[32]  Jessica C. Ebert,et al.  Accurate whole genome sequencing and haplotyping from10-20 human cells , 2012, Nature.

[33]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[34]  N. Siva.  1000 Genomes project , 2008, Nature Biotechnology.

[35]  Thomas Meitinger,et al.  Loss-of-function mutations in SLC30A8 protect against type 2 diabetes , 2014, Nature Genetics.

[36]  L. Hurst.  The Ka/Ks ratio: diagnosing the form of sequence evolution. , 2002, Trends in genetics : TIG.

[37]  D. Goldstein,et al.  Uncovering the roles of rare variants in common disease through whole-genome sequencing , 2010, Nature Reviews Genetics.

[38]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[39]  N. Cox,et al.  Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS , 2010, PLoS genetics.

[40]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[41]  Paul Flicek,et al.  The functional spectrum of low-frequency coding variation , 2011, Genome Biology.

[42]  D. MacArthur,et al.  Negligible impact of rare autoimmune-locus coding-region variants on missing heritability , 2013, Nature.

[43]  Pedro G. Ferreira,et al.  Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.

[44]  Eleftheria Zeggini,et al.  In search of low-frequency and rare variants affecting complex traits , 2013, Human molecular genetics.

[45]  D. MacArthur,et al.  Loss-of-function variants in the genomes of healthy humans. , 2010, Human molecular genetics.

[46]  Roderic Guigó,et al.  The GEM mapper: fast, accurate and versatile alignment by filtration , 2012, Nature Methods.