A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

Abstract

There is a complex relationship between the evolution of segmental duplications and rearrangements associated with human disease. We performed a detailed analysis of one region on chromosome 16p12.1 associated with neurocognitive disease and identified one of the largest structural inconsistencies in the human reference assembly. Various genomic analyses show that all examined humans are homozygously inverted relative to the reference genome for a 1.1-Mb region on 16p12.1. We determined that this assembly discrepancy stems from two common structural configurations with worldwide frequencies of 17.6% (S1) and 82.4% (S2). This polymorphism arose from the rapid integration of segmental duplications, precipitating two local inversions within the human lineage over the last 10 million years. The two human haplotypes differ by 333 kb of additional duplicated sequence present in S2 but not in S1. Notably, we show that the S2 configuration harbors directly oriented duplications, specifically predisposing this chromosome to disease-associated rearrangement.

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Figure 1: Alternative structural configurations of the 16p12.1 region.
Figure 2: Array CGH data for 16p12.1 microdeletion samples and control HapMap samples (NA15510, NA12004 and NA18555).
Figure 3: Expansion and multiple inversions of the 16p12.1 region in humans and the syntenic regions in nonhuman primates during primate evolution.
Figure 4: Regions of segmental duplication based on read-depth mapping of whole-genome shotgun sequences against the human genome.

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Accessions

EMBL/GenBank/DDBJ

GenBank/EMBL/DDBJ

Gene Expression Omnibus

NCBI Reference Sequence

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Acknowledgements

We thank P. Sudmant for useful discussions, G.M. Cooper and T. Brown for critical review of the manuscript and L. Zhou, Y. Fu, R. Shi, J. Wu, S. Shaull and B.A. Roe for sequencing of clone AC120780. This work was supported by a US National Science Foundation Graduate Research Fellowship (to J.M.K.) and a Marie Curie fellowship (FP7 to T.M.-B.), and by the US National Institutes of Health (grants T32 GM07215 and 5T15 LM007359 to B.T., HG000225 to D.C.S. and HG002385 to E.E.E.). E.E.E. is an investigator of the Howard Hughes Medical Institute.

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F.A. and E.E.E. designed the study. F.A. performed FISH experiments and constructed shotgun sequencing libraries. J.M.K. performed sequence analysis and haplotype reconstructions. B.T. and D.C.S. performed optical mapping analysis. T.M.-B., T.A.G. and R.K.W. performed nonhuman primate BAC clone sequencing and analysis. M.V. performed FISH experiments on stretched chromosomes. C.A. performed Illumina sequencing data analysis. S.G., C.D.C. and L.V. performed high-density array CGH experiments. M.M. performed PCR experiments. J.A.R., B.C.B. and L.G.S. contributed to 16p12.1 microdeletion data collection. F.A., J.M.K. and E.E.E. contributed to data interpretation. F.A. and E.E.E. wrote the manuscript.

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Correspondence to Evan E Eichler.

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E.E.E. is a member of the Scientific Advisory Board of Pacific Biosciences. J.A.R. and B.C.B. are employees of PerkinElmer (previously Signature Genomic Laboratories). L.G.S. is an employee of PerkinElmer, sits on the Board of the Washington Biotechnology & Biomedical Association and sits on the Board of the American College of Medical Genetics Foundation.

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Antonacci, F., Kidd, J., Marques-Bonet, T. et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat Genet 42, 745–750 (2010). https://doi.org/10.1038/ng.643

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