Personalized copy number and segmental duplication maps using next-generation sequencing

Alkan, Can; Kidd, Jeffrey M.; Marquès‐Bonet, Tomàs; Aksay, Gozde; Antonacci, Francesca; Hormozdiari, Fereydoun; Kitzman, Jacob O.; Baker, Carl; Malig, Maika; Mutlu, Onur; Şahinalp, S. Cenk; Gibbs, Richard A.; Eichler, Evan E.

doi:10.1038/ng.437

Cited by 648 publications

(647 citation statements)

References 38 publications

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“…5 Interphase FISH has been used to determine relative haploid copy numbers but becomes impractical when amplicon size is small and copy number very high. 32 Further investigations will be needed of EV and non-EV carriers in larger families using quantitative allele-specific copy number techniques 33 to confirm or exclude our proposal.…”

Section: Discussionmentioning

confidence: 79%

Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

et al. 2013

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Copy number variants visible with the light microscope have been described as euchromatic variants (EVs) and EVs with extra G-light material at 8q21.2 have been reported only once before. We report four further patients with EVs of 8q21.2 ascertained for clinical (3) or reproductive reasons (1). Enhanced signal strength from two overlapping bacterial artificial chromosomes (BACs) and microarray analysis mapped the EV to a 284-kb interval in the reference genome. This interval consists of a sequence gap flanked by segmental duplications that contain the 12-kb components of one of the largest Variable Number Tandem Repeat arrays in the human genome. Using digital NanoString technology with a custom probe for the RNA exonuclease 1 homologue (S. cerevisiae)-like 1 (REXO1L1) gene within each 12-kb repeat, significantly enhanced diploid copy numbers of 270 and 265 were found in an EV family and a median diploid copy number of 166 copies in 216 controls. These 8q21.2 EVs are not thought to have clinical consequences as the phenotypes of the probands were inconsistent, those referred for reproductive reasons were otherwise phenotypically normal and the REXO1L1 gene has no known disease association. This EV was found in 4/3078 (1 in 770) consecutive referrals for chromosome analysis and needs to be distinguished from pathogenic imbalances of medial 8q. The REXO1L1 gene product is a marker of hepatitis C virus (HCV) infection and a possible association between REXO1L1 copy number and susceptibility to HCV infection, progression or response to treatment has not yet been excluded.

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Section: Discussionmentioning

confidence: 79%

Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

et al. 2013

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“…Local variation in read depth has been benchmarked as a reliable method for the identification and quantification of CNV 15,16 . We modified the approach to quantify dosage of the rRNA encoding loci, as the read depth coverage of the rDNA components relative to baseline read depth of single copy sequences (see Fig.…”

Section: Resultsmentioning

confidence: 99%

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

et al. 2014

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Ribosomes are essential intracellular machines composed of proteins and RNA molecules. The DNA sequences (rDNA) encoding ribosomal RNAs (rRNAs) are tandemly repeated and give origin to the nucleolus. Here we develop a computational method for estimating rDNA dosage (copy number) and mitochondrial DNA abundance using whole-genome short-read DNA sequencing. We estimate these attributes across hundreds of human genomes and their association with global gene expression. The analyses uncover abundant variation in rDNA dosage that is coupled with the expression of hundreds of functionally coherent gene sets. These include associations with genes coding for chromatin components that target the nucleolus, including CTCF and HP1b. Finally, the data show an inverse association between rDNA dosage and mitochondrial DNA abundance that is manifested across genotypes. Our findings uncover a novel and cryptic source of hypervariable genomic diversity with global regulatory consequences (ribosomal eQTL) in humans. The variation provides a mechanism for cellular homeostasis and for rapid and reversible adaptation.

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“…We were fortunate in this experiment that one of two sequencing approaches that we used detected the presence of the disease-causing mutation, albeit by a somewhat indirect mechanism. Many groups are working to overcome these analytical blind spots (26,27), and as these methods are perfected, many more Short INterspersed Elementsand Long INterspersed Elements-associated mutations will undoubtedly be identified by exome sequencing.…”

Section: Mak Is Expressed In Both Rod and Cone Photoreceptors In The mentioning

confidence: 99%

Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase ( MAK ) as a cause of retinitis pigmentosa

Tucker

Scheetz

Mullins

et al. 2011

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

193

191

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Retinitis pigmentosa (RP) is a genetically heterogeneous heritable disease characterized by apoptotic death of photoreceptor cells. We used exome sequencing to identify a homozygous Alu insertion in exon 9 of male germ cell-associated kinase (MAK) as the cause of disease in an isolated individual with RP. Screening of 1,798 unrelated RP patients identified 20 additional probands homozygous for this insertion (1.2%). All 21 affected probands are of Jewish ancestry. MAK encodes a kinase involved in the regulation of photoreceptor-connecting cilium length. Immunohistochemistry of human donor tissue revealed that MAK is expressed in the inner segments, cell bodies, and axons of rod and cone photoreceptors. Several isoforms of MAK that result from alternative splicing were identified. Induced pluripotent stem cells were derived from the skin of the proband and a patient with non-MAK-associated RP (RP control). In the RP control individual, we found that a transcript lacking exon 9 was predominant in undifferentiated cells, whereas a transcript bearing exon 9 and a previously unrecognized exon 12 predominated in cells that were differentiated into retinal precursors. However, in the proband with the Alu insertion, the developmental switch to the MAK transcript bearing exons 9 and 12 did not occur. In addition to showing the use of induced pluripotent stem cells to efficiently evaluate the pathogenicity of specific mutations in relatively inaccessible tissues like retina, this study reveals algorithmic and molecular obstacles to the discovery of pathogenic insertions and suggests specific changes in strategy that can be implemented to more fully harness the power of sequencing technologies.

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Personalized copy number and segmental duplication maps using next-generation sequencing

Cited by 648 publications

References 38 publications

Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase ( MAK ) as a cause of retinitis pigmentosa

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