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Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions

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Abstract

Over 900 genes have been annotated within duplicated regions of the human genome, yet their functions and potential roles in disease remain largely unknown. One major obstacle has been the inability to accurately and comprehensively assay genetic variation for these genes in a high-throughput manner. We developed a sequencing-based method for rapid and high-throughput genotyping of duplicated genes using molecular inversion probes designed to target unique paralogous sequence variants. We applied this method to genotype all members of two gene families, SRGAP2 and RH, among a diversity panel of 1,056 humans. The approach could accurately distinguish copy number in paralogs having up to 99.6% sequence identity, identify small gene-disruptive deletions, detect single-nucleotide variants, define breakpoints of unequal crossover and discover regions of interlocus gene conversion. The ability to rapidly and accurately genotype multiple gene families in thousands of individuals at low cost enables the development of genome-wide gene conversion maps and 'unlocks' many previously inaccessible duplicated genes for association with human traits.

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Figure 1: MIP copy-number genotyping assay for duplicated genes.
Figure 2: Accuracy of paralog-specific copy-number genotyping.
Figure 3: Resolution of complex structural variation in SRGAP2.
Figure 4: Detection of gene conversion at the RH locus.
Figure 5: Resolution of nonallelic homologous recombination (NAHR)-associated RHD deletion and duplication breakpoints.
Figure 6: Extensive interlocus gene conversion between SRGAP2 paralogs.

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  • 13 August 2013

    In the version of this article initially published online, the affiliation for Corrado Romano was incorrect. The correct affiliation is: Pediatrics and Medical Genetics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Associazione Oasi Maria Santissima, Troina, Italy. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank J. Kitzman for early ideas and enthusiasm for the project; P. Sudmant, E. Karakoc, F. Hormozdiari, B. Dumont and O. Penn for thoughtful discussion; L. Vives, K. Mohajeri and C. Lee for technical assistance; and T. Brown for assistance with manuscript preparation. X.N. is supported by a US National Science Foundation Graduate Research Fellowship under grant no. DGE-1256082. This work was supported by US National Institutes of Health grants HG004120 and HG002385 to E.E.E. E.E.E. is supported by the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Contributions

X.N., J.S. and E.E.E. designed the study. X.N. and B.J.O. designed the MIPs. X.N. performed capture experiments, wrote analysis software and analyzed data. F.A. performed FISH experiments. J.H. contributed to the analysis software, prepared it for public access and identified SUNs from the reference genome. M.F. and C.R. contributed to sample collection. X.N. and E.E.E. wrote the paper, with input and approval from all coauthors.

Corresponding author

Correspondence to Evan E Eichler.

Ethics declarations

Competing interests

E.E.E. is on the scientific advisory boards for Pacific Biosciences, Inc., SynapDx Corp. and DNAnexus, Inc.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Tables 1 and 7–10 (PDF 3550 kb)

Supplementary Table 2

MIP pooling scheme and sequences. (XLSX 25 kb)

Supplementary Table 3

Comparison of MIP-based paralog-specific copy number estimates with orthogonal data. (XLSX 22 kb)

Supplementary Table 4

Comparison of MIP-based genotyping between replicate experiments for 73 individuals where at least 1 technical replicate was performed. (XLSX 23 kb)

Supplementary Table 5

Frequencies of SRGAP2 and RH duplications, deletions, and interlocus gene conversions in 9 HapMap populations. (XLSX 16 kb)

Supplementary Table 6

Single nucleotide variants detected and genotyped for NA18507 and comparison with whole-genome sequence data. (XLSX 15 kb)

Supplementary Table 11

Comparison of MIP-based paralog-specific detected internal variants with orthogonal data. (XLSX 11 kb)

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Nuttle, X., Huddleston, J., O'Roak, B. et al. Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nat Methods 10, 903–909 (2013). https://doi.org/10.1038/nmeth.2572

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