Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics.

Genetics in Medicine : Official Journal of the American College of Medical Genetics
Zirui DongKwong Wai Choy

Abstract

Recent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected. The 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparent BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold). With this approach, we detected four reciprocal balanced translocations and four inversions, ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and polymerase chain reaction studies. One of these DNAs has a subtle translocation that is not readily identified by chromosome analysis because of the similarity of the banding patterns and size of exchanged segments, and another results in disruption of a...Continue Reading

References

Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Oct 3, 2002·Molecular Human Reproduction·M Oliver-BonetJ Benet
Dec 4, 2002·European Journal of Human Genetics : EJHG·Caroline Mackie Ogilvie, Paul N Scriven
Oct 3, 2007·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·David H Ledbetter, Christa Lese Martin
Nov 7, 2008·Nature·Jun WangJian Wang
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Sep 18, 2010·Nature Reviews. Genetics·Matthew MeyersonGad Getz
Oct 27, 2010·PLoS Genetics·Ni HuangMatthew E Hurles
Mar 1, 2012·Human Mutation·Matthew D ShirleyJonathan Pevsner
Sep 8, 2012·Nature·Robert E ThurmanJohn A Stamatoyannopoulos
Nov 30, 2012·Nucleic Acids Research·Kate R RosenbloomW James Kent
Dec 12, 2012·The New England Journal of Medicine·Michael E TalkowskiCynthia C Morton
May 30, 2013·Nature Genetics·UNKNOWN GTEx Consortium
Mar 13, 2014·Nature Reviews. Genetics·Daria ShlyuevaAlexander Stark
Jan 2, 2015·Evolutionary Applications·Robert Ekblom, Jochen B W Wolf
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Oct 4, 2015·Nature·Peter H SudmantJan O Korbel
Oct 7, 2015·Trends in Biochemical Sciences·Agnel Sfeir, Lorraine S Symington
Jan 29, 2016·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Zirui DongZhengfeng Xu
Jan 31, 2016·Reproduction : the Official Journal of the Society for the Study of Fertility·Baoheng GuiLingqian Wu
Mar 1, 2016·Nature Reviews. Genetics·Claudia M B Carvalho, James R Lupski
May 18, 2016·Nature Reviews. Genetics·Sara GoodwinW Richard McCombie

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Citations

Jul 7, 2018·Current Protocols in Human Genetics·Cui SongJun Shen
Apr 27, 2019·Journal of Medical Genetics·David BickJohn Belmont
Aug 27, 2019·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Huilin WangKwong Wai Choy
Dec 4, 2019·Plant Methods·Zhaozhao DaiMeizhong Luo
Jun 25, 2020·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Bo YuanWeimin Bi
Jun 8, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Zirui DongYuan Jiang
Jul 31, 2020·Human Genetics·Zirui DongKwong Wai Choy
Jan 16, 2021·Metabolites·Marc Feuermann On Behalf Of The UniProt Consortium
Mar 22, 2020·Ultrasound in Obstetrics & Gynecology : the Official Journal of the International Society of Ultrasound in Obstetrics and Gynecology·Xiaofan ZhuKwong Wai Choy
Mar 28, 2021·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Zirui DongKwong Wai Choy
Jul 9, 2021·American Journal of Human Genetics·Tuomo MantereLaïla El Khattabi

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Datasets Mentioned

BETA
GSE94043
NA20759
GM12878

Methods Mentioned

BETA
Assay
PCR
RNA-seq
ChIP-seq

Software Mentioned

HISAT ( Hierarchical Indexing for Spliced Alignment of Transcr...
SpectrumOrange
SpectrumRed
Primer3 Web
BLAT
Samtools
- Blast
SpectrumGreen
Integrative Genomics Viewer
Bowtie

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