Advertisement

Identification of Low Allele Frequency Mosaic Mutations in Alzheimer Disease

  • Carlo Sala FrigerioEmail author
  • Mark Fiers
  • Thierry Voet
  • Bart De StrooperEmail author
Protocol
Part of the Neuromethods book series (NM, volume 131)

Abstract

Germline mutations ofAPP,PSEN1, andPSEN2 genes cause autosomal dominant Alzheimer disease (AD). Somatic variants of the same genes may underlie pathogenesis in sporadic AD, which is the most prevalent form of the disease. Importantly, such somatic variants may be present at very low allelic frequency, confined to the brain, and are thus very difficult or impossible to detect in blood-derived DNA. Ever-refined methodologies to identify mutations present in a fraction of the DNA of the original tissue are rapidly transforming our understanding of DNA mutation and their role in complex pathologies such as tumors. These methods stand poised to test to what extend somatic variants may play a role in AD and other neurodegenerative diseases.

Key words

Single- cell sequencing Mosaicism Somatic variant Alzheimer’s disease Parkinson’s disease 

References

  1. 1.
    Cruts M, Theuns J, Van Broeckhoven C (2012) Locus-specific mutation databases for neurodegenerative brain diseases. Hum Mutat 33:1340–1344. doi: 10.1002/humu.22117 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Rovelet-Lecrux A, Hannequin D, Raux G et al (2006) APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat Genet 38:24–26. doi: 10.1038/ng1718 CrossRefPubMedGoogle Scholar
  3. 3.
    Lodato MA, Woodworth MB, Lee S et al (2015) Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350:94–98. doi: 10.1126/science.aab1785 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Upton KR, Gerhardt DJ, Jesuadian JS et al (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161:228–239. doi: 10.1016/j.cell.2015.03.026 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Evrony GD, Lee E, Park PJ, Walsh CA (2016) Resolving rates of mutation in the brain using single-neuron genomics. elife. doi: 10.7554/eLife.12966
  6. 6.
    McConnell MJ, Lindberg MR, Brennand KJ et al (2013) Mosaic copy number variation in human neurons. Science 342:632–637. doi: 10.1126/science.1243472 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Evrony GD, Cai X, Lee E et al (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151:483–496. doi: 10.1016/j.cell.2012.09.035 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Aguzzi A, Lakkaraju AK (2015) Cell biology of prions and prionoids: a status report. Trends Cell Biol 26(1):40–51. doi: 10.1016/j.tcb.2015.08.007. CrossRefPubMedGoogle Scholar
  9. 9.
    Brettschneider J, Del Tredici K, Lee VM, Trojanowski JQ (2015) Spreading of pathology in neurodegenerative diseases: a focus on human studies. Nat Rev Neurosci 16:109–120. doi: 10.1038/nrn3887 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Auton A, Brooks LD, Durbin RM et al (2015) A global reference for human genetic variation. Nature 526:68–74. doi: 10.1038/nature15393 CrossRefPubMedGoogle Scholar
  11. 11.
    Nussbaum R, McInnes RR, Willard HF (2007) Thompson & Thompson genetics in medicine, 7th edn. Saunders, PhiladelphiaGoogle Scholar
  12. 12.
    Alzualde A, Moreno F, Martinez-Lage P et al (2010) Somatic mosaicism in a case of apparently sporadic Creutzfeldt-Jakob disease carrying a de novo D178N mutation in the PRNP gene. Am J Med Genet B Neuropsychiatr Genet 153B:1283–1291. doi: 10.1002/ajmg.b.31099 CrossRefPubMedGoogle Scholar
  13. 13.
    Tsiatis AC, Norris-Kirby A, Rich RG et al (2010) Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations: diagnostic and clinical implications. J Mol Diagn 12:425–432. doi: 10.2353/jmoldx.2010.090188 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Jamuar SS, Lam AT, Kircher M et al (2014) Somatic mutations in cerebral cortical malformations. N Engl J Med 371:733–743. doi: 10.1056/NEJMoa1314432 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Macaulay IC, Voet T (2014) Single cell genomics: advances and future perspectives. PLoS Genet 10(1):e1004126. doi: 10.1371/journal.pgen.1004126 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Gawad C, Koh W, Quake SR (2016) Single-cell genome sequencing: current state of the science. Nat Rev Genet 17:175–188. doi: 10.1038/nrg.2015.16 CrossRefPubMedGoogle Scholar
  17. 17.
    Braak H, Braak E (1991) Neuropathological stageing of Alzheimer-related changes. Acta Neuropathol 82:239–259CrossRefPubMedGoogle Scholar
  18. 18.
    Sala Frigerio C, Lau P, Troakes C et al (2015) On the identification of low allele frequency mosaic mutations in the brains of Alzheimer’s disease patients. Alzheimers Dement 11:1265–1276. doi: 10.1016/j.jalz.2015.02.007 CrossRefPubMedGoogle Scholar
  19. 19.
    Small SA, Duff K (2008) Linking Abeta and tau in late-onset Alzheimer’s disease: a dual pathway hypothesis. Neuron 60:534–542. doi: 10.1016/j.neuron.2008.11.007 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Li H, Durbin R (2010) Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics 26:589–595. doi: 10.1093/bioinformatics/btp698 CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. doi: 10.1101/gr.107524.110 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993. doi: 10.1093/bioinformatics/btr509 CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Koboldt DC, Zhang Q, Larson DE et al (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22:568–576. doi: 10.1101/gr.129684.111 CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Cingolani P, Platts A, Wang le L et al (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Flying 6:80–92. doi: 10.4161/fly.19695 Google Scholar
  26. 26.
    Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:e164. doi: 10.1093/nar/gkq603 CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Kanagawa T (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96:317–323. doi: 10.1016/S1389-1723(03)90130-7 CrossRefPubMedGoogle Scholar
  28. 28.
    Gundry M, Vijg J (2011) Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat Res 729:1–15. doi: 10.1016/j.mrfmmm.2011.10.001 CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Schmitt MW, Kennedy SR, Salk JJ et al (2012) Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A 109:14508–14513. doi: 10.1073/pnas.1208715109 CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Smith EN, Jepsen K, Khosroheidari M et al (2014) Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol 15:420. doi: 10.1186/s13059-014-0420-4 CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Kennedy SR, Schmitt MW, Fox EJ et al (2014) Detecting ultralow-frequency mutations by duplex sequencing. Nat Protoc 9:2586–2606. doi: 10.1038/nprot.2014.170 CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Lou DI, Hussmann JA, McBee RM et al (2013) High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc Natl Acad Sci U S A 110:19872–19877. doi: 10.1073/pnas.1319590110 CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Dean FB, Hosono S, Fang L et al (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99:5261–5266. doi: 10.1073/pnas.08208949999/8/5261 CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    de Bourcy CF, De Vlaminck I, Kanbar JN et al (2014) A quantitative comparison of single-cell whole genome amplification methods. PLoS One 9:e105585. doi: 10.1371/journal.pone.0105585PONE-D-14-24544 CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Zafar H, Wang Y, Nakhleh L, et al (2016) Monovar: single-nucleotide variant detection in single cells. doi: 10.1038/pj.2016.37
  36. 36.
    Roth A, McPherson A, Laks E et al (2016) Clonal genotype and population structure inference from single-cell tumor sequencing. Nat Methods 13:573–576. doi: 10.1038/nmeth.3867 CrossRefPubMedGoogle Scholar
  37. 37.
    Eirew P, Steif A, Khattra J et al (2014) Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature 518:422–426. doi: 10.1038/nature13952 CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Hindson BJ, Ness KD, Masquelier DA et al (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 83:8604–8610. doi: 10.1021/ac202028g CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Geller LN, Potter H (1999) Chromosome missegregation and trisomy 21 mosaicism in Alzheimer’s disease. Neurobiol Dis 6:167–179. doi: 10.1006/nbdi.1999.0236 CrossRefPubMedGoogle Scholar
  40. 40.
    Beck JA, Poulter M, Campbell TA et al (2004) Somatic and germline mosaicism in sporadic early-onset Alzheimer’s disease. Hum Mol Genet 13:1219–1224. doi: 10.1093/hmg/ddh134ddh134 CrossRefPubMedGoogle Scholar
  41. 41.
    Proukakis C, Houlden H, Schapira AH (2013) Somatic alpha-synuclein mutations in Parkinson’s disease: hypothesis and preliminary data. Mov Disord 28:705–712. doi: 10.1002/mds.25502 CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Proukakis C, Shoaee M, Morris J et al (2014) Analysis of Parkinson’s disease brain-derived DNA for alpha-synuclein coding somatic mutations. Mov Disord 29:1060–1064. doi: 10.1002/mds.25883 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.VIB Center for Brain & Disease ResearchLeuvenBelgium
  2. 2.Center for Human GeneticsUniversitaire ziekenhuizen and LIND, KU LeuvenLeuvenBelgium
  3. 3.Department of Human GeneticsUniversity of Leuven, KU LeuvenLeuvenBelgium
  4. 4.Wellcome Trust Sanger InstituteHinxtonUK
  5. 5.Dementia Research Institute(UK-DRI)University College LondonLondonUK

Personalised recommendations