Human Genetics

, Volume 134, Issue 6, pp 589–603 | Cite as

Characterization of 26 deletion CNVs reveals the frequent occurrence of micro-mutations within the breakpoint-flanking regions and frequent repair of double-strand breaks by templated insertions derived from remote genomic regions

  • Ye Wang
  • Peiqiang Su
  • Bin Hu
  • Wenjuan Zhu
  • Qibin Li
  • Ping Yuan
  • Jiangchao Li
  • Xinyuan Guan
  • Fucheng Li
  • Xiangyi Jing
  • Ru Li
  • Yongling Zhang
  • Claude Férec
  • David N. Cooper
  • Jun Wang
  • Dongsheng Huang
  • Jian-Min Chen
  • Yiming Wang
Original Investigation

Abstract

Copy number variations (CNVs) have increasingly been reported to cause, or predispose to, human disease. However, a large fraction of these CNVs have not been accurately characterized at the single-base-pair level, thereby hampering a better understanding of the mutational mechanisms underlying CNV formation. Here, employing a composite pipeline method derived from various inference-based programs, we have characterized 26 deletion CNVs [including three novel pathogenic CNVs involving an autosomal gene (EXT2) causing hereditary osteochondromas and an X-linked gene (CLCN5) causing Dent disease, as well as 23 CNVs previously identified by inference from a cohort of Canadian autism spectrum disorder families] to the single-base-pair level of accuracy from whole-genome sequencing data. We found that breakpoint-flanking micro-mutations (within 22 bp of the breakpoint) are present in a significant fraction (5/26; 19 %) of the deletion CNVs. This analysis also provided evidence that a recently described error-prone form of DNA repair (i.e., repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome) not only causes human genetic disease but also impacts on human genome evolution. Our findings illustrate the importance of precise CNV breakpoint delineation for understanding the underlying mutational mechanisms and have implications for primer design in relation to the detection of deletion CNVs in clinical diagnosis.

Supplementary material

439_2015_1539_MOESM1_ESM.docx (2.8 mb)
Supplementary material 1 (DOCX 2891 kb)

References

  1. Abyzov A, Urban AE, Snyder M, Gerstein M (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21:974–984CrossRefPubMedCentralPubMedGoogle Scholar
  2. Arlt MF, Rajendran S, Birkeland SR, Wilson TE, Glover TW (2012) De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining. PLoS Genet 8:e1002981CrossRefPubMedCentralPubMedGoogle Scholar
  3. Audrézet MP, Chen JM, Raguénès O, Chuzhanova N, Giteau K, Le Maréchal C, Quéré I, Cooper DN, Férec C (2004) Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms. Hum Mutat 23:343–357CrossRefPubMedGoogle Scholar
  4. Bovee JV (2008) Multiple osteochondromas. Orphanet J Rare Dis 3:3CrossRefPubMedCentralPubMedGoogle Scholar
  5. Cardoso-Moreira M, Arguello JR, Clark AG (2012) Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing. Genome Biol 13:R119CrossRefPubMedCentralPubMedGoogle Scholar
  6. Carvalho CM, Pehlivan D, Ramocki MB, Fang P, Alleva B, Franco LM, Belmont JW, Hastings PJ, Lupski JR (2013) Replicative mechanisms for CNV formation are error prone. Nat Genet 45:1319–1326CrossRefPubMedGoogle Scholar
  7. Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN (2005) Complex gene rearrangements caused by serial replication slippage. Hum Mutat 26:125–134CrossRefPubMedGoogle Scholar
  8. Chen JM, Cooper DN, Chuzhanova N, Férec C, Patrinos GP (2007) Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 8:762–775CrossRefPubMedGoogle Scholar
  9. Chen JM, Férec C, Cooper DN (2009a) Closely spaced multiple mutations as potential signatures of transient hypermutability in human genes. Hum Mutat 30:1435–1448CrossRefPubMedGoogle Scholar
  10. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER (2009b) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681CrossRefPubMedCentralPubMedGoogle Scholar
  11. Chen JM, Cooper DN, Férec C, Kehrer-Sawatzki H, Patrinos GP (2010) Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol 20:222–233CrossRefPubMedGoogle Scholar
  12. Chen JM, Férec C, Cooper DN (2013) Patterns and mutational signatures of tandem base substitutions causing human inherited disease. Hum Mutat 34:1119–1130CrossRefPubMedGoogle Scholar
  13. Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, Turner DJ, Hurles ME (2010) Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet 42:385–391CrossRefPubMedCentralPubMedGoogle Scholar
  14. De S, Babu MM (2010) A time-invariant principle of genome evolution. Proc Natl Acad Sci USA 107:13004–13009CrossRefPubMedCentralPubMedGoogle Scholar
  15. Deem A, Keszthelyi A, Blackgrove T, Vayl A, Coffey B, Mathur R, Chabes A, Malkova A (2011) Break-induced replication is highly inaccurate. PLoS Biol 9:e1000594CrossRefPubMedCentralPubMedGoogle Scholar
  16. Devuyst O, Thakker RV (2010) Dent’s disease. Orphanet J Rare Dis 5:28CrossRefPubMedCentralPubMedGoogle Scholar
  17. Hastings PJ, Ira G, Lupski JR (2009) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5:e1000327CrossRefPubMedCentralPubMedGoogle Scholar
  18. Hicks WM, Kim M, Haber JE (2010) Increased mutagenesis and unique mutation signature associated with mitotic gene conversion. Science 329:82–85CrossRefPubMedCentralPubMedGoogle Scholar
  19. Huang S, Yu T, Chen Z, Yuan S, Chen S, Xu A (2012) More single-nucleotide mutations surround small insertions than small deletions in primates. Hum Mutat 33:1099–1106CrossRefPubMedGoogle Scholar
  20. Iraqui I, Chekkal Y, Jmari N, Pietrobon V, Freon K, Costes A, Lambert SA (2012) Recovery of arrested replication forks by homologous recombination is error-prone. PLoS Genet 8:e1002976CrossRefPubMedCentralPubMedGoogle Scholar
  21. Jiang YH, Yuen RK, Jin X, Wang M, Chen N, Wu X, Ju J, Mei J, Shi Y, He M, Wang G, Liang J, Wang Z, Cao D, Carter MT, Chrysler C, Drmic IE, Howe JL, Lau L, Marshall CR, Merico D, Nalpathamkalam T, Thiruvahindrapuram B, Thompson A, Uddin M, Walker S, Luo J, Anagnostou E, Zwaigenbaum L, Ring RH, Wang J, Lajonchere C, Shih A, Szatmari P, Yang H, Dawson G, Li Y, Scherer SW (2013) Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet 93:249–263CrossRefPubMedCentralPubMedGoogle Scholar
  22. Jovelin R, Cutter AD (2013) Fine-scale signatures of molecular evolution reconcile models of indel-associated mutation. Genome Biol Evol 5:978–986CrossRefPubMedCentralPubMedGoogle Scholar
  23. Keskin H, Shen Y, Huang F, Patel M, Yang T, Ashley K, Mazin AV, Storici F (2014) Transcript-RNA-templated DNA recombination and repair. Nature 515:436–439CrossRefPubMedGoogle Scholar
  24. Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, Kallicki J, Kaul R, Wilson RK, Eichler EE (2010) A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143:837–847CrossRefPubMedCentralPubMedGoogle Scholar
  25. Lathrop GM, Lalouel JM (1984) Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet 36:460–465PubMedCentralPubMedGoogle Scholar
  26. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760CrossRefPubMedCentralPubMedGoogle Scholar
  27. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedCentralPubMedGoogle Scholar
  28. Lieber MR (2008) The mechanism of human nonhomologous DNA end joining. J Biol Chem 283:1–5CrossRefPubMedGoogle Scholar
  29. Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, Bacino CA, Campos-Acevedo LD, Delgado MR, Freedenberg D, Garnica A, Grebe TA, Hernandez-Almaguer D, Immken L, Lalani SR, McLean SD, Northrup H, Scaglia F, Strathearn L, Trapane P, Kang SH, Patel A, Cheung SW, Hastings PJ, Stankiewicz P, Lupski JR, Bi W (2011) Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146:889–903CrossRefPubMedCentralPubMedGoogle Scholar
  30. McVey M, Lee SE (2008) MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings. Trends Genet 24:529–538CrossRefPubMedGoogle Scholar
  31. Onozawa M, Zhang Z, Kim YJ, Goldberg L, Varga T, Bergsagel PL, Kuehl WM, Aplan PD (2014) Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome. Proc Natl Acad Sci USA 111:7729–7734CrossRefPubMedCentralPubMedGoogle Scholar
  32. Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28:i333–i339CrossRefPubMedCentralPubMedGoogle Scholar
  33. Shah KA, Shishkin AA, Voineagu I, Pavlov YI, Shcherbakova PV, Mirkin SM (2012) Role of DNA polymerases in repeat-mediated genome instability. Cell Rep 2:1088–1095CrossRefPubMedCentralPubMedGoogle Scholar
  34. Smith CE, Llorente B, Symington LS (2007) Template switching during break-induced replication. Nature 447:102–105CrossRefPubMedGoogle Scholar
  35. Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192CrossRefPubMedCentralPubMedGoogle Scholar
  36. Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ (2008) Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455:105–108CrossRefPubMedGoogle Scholar
  37. Yalcin B, Wong K, Bhomra A, Goodson M, Keane TM, Adams DJ, Flint J (2012) The fine-scale architecture of structural variants in 17 mouse genomes. Genome Biol 13:R18CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Ye Wang
    • 1
    • 2
  • Peiqiang Su
    • 2
  • Bin Hu
    • 1
  • Wenjuan Zhu
    • 3
  • Qibin Li
    • 3
  • Ping Yuan
    • 1
    • 4
  • Jiangchao Li
    • 5
    • 6
  • Xinyuan Guan
    • 5
    • 7
  • Fucheng Li
    • 1
  • Xiangyi Jing
    • 1
    • 8
  • Ru Li
    • 8
  • Yongling Zhang
    • 8
  • Claude Férec
    • 9
    • 10
    • 11
    • 12
  • David N. Cooper
    • 13
  • Jun Wang
    • 3
    • 14
  • Dongsheng Huang
    • 15
  • Jian-Min Chen
    • 9
    • 10
    • 11
  • Yiming Wang
    • 1
    • 3
  1. 1.Department of Medical Genetics, Zhongshan School of Medicine and Center for Genome ResearchSun Yat-Sen UniversityGuangzhouChina
  2. 2.Department of Orthopedics, First Affiliated HospitalSun Yat-Sen UniversityGuangzhouChina
  3. 3.Beijing Genomics Institute (BGI)-ShenzhenShenzhenChina
  4. 4.Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial HospitalSun Yat-Sen UniversityGuangzhouChina
  5. 5.State Key Laboratory of Oncology in Southern China, Cancer CenterSun Yat-Sen UniversityGuangzhouChina
  6. 6.Vascular Biology Research InstituteGuangdong Pharmaceutical UniversityGuangzhouChina
  7. 7.Department of Clinical OncologyThe University of Hong KongHong KongChina
  8. 8.Prenatal Diagnostic CenterGuangzhou Women and Children Medical Center affiliated to Guangzhou Medical UniversityGuangzhouChina
  9. 9.Institut National de la Santé et de la Recherche Médicale (INSERM), U1078BrestFrance
  10. 10.Etablissement Français du Sang (EFS) - BretagneBrestFrance
  11. 11.Faculté de Médecine et des Sciences de la SantéUniversité de Bretagne Occidentale (UBO)BrestFrance
  12. 12.Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Universitaire (CHU) BrestHôpital MorvanBrestFrance
  13. 13.Institute of Medical Genetics, School of MedicineCardiff UniversityCardiffUK
  14. 14.Department of BiologyUniversity of CopenhagenCopenhagenDenmark
  15. 15.Department of Orthopedics, Sun Yat-sen Memorial HospitalSun Yat-Sen UniversityGuangzhouChina

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