Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing

Genomics
Usha R DuttaAshwin Dalal

Abstract

Disease associated chromosomal rearrangements often have break points located within disease causing genes or in their vicinity. The purpose of this study is to characterize a balanced reciprocal translocation in a girl with intellectual disability and seizures by positional cloning and whole genome sequencing. The translocation was identification by G- banding and confirmed by WCP FISH. Fine mapping using BAC clones and whole genome sequencing using Oxford nanopore long read sequencing technology for a 1.46 X coverage of the genome was done. The positional cloning showed split signals with BAC RP11-943 J20. Long read sequencing analysis of chimeric reads carrying parts of chromosomes X and 20 helped to identify the breakpoints to be in intron 2 of ARHGEF9 gene on Xp11.1 and on 20p13 between RASSF2 and SLC23A2 genes. This is the first report of translocation which successfully delineated to single base resolution using Nanopore sequencing. The genotype-phenotype correlation is discussed.

References

Oct 6, 1997·Genes & Development·L Van Aelst, C D'Souza-Schorey
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Oct 3, 2002·Molecular Human Reproduction·M Oliver-BonetJ Benet
Mar 19, 2004·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Kazusaku KamiyaKazuhiro Yamakawa
Mar 18, 2005·Cancer Genetics and Cytogenetics·John O'ReillyPaul Cannell
Sep 1, 2007·Current Opinion in Psychiatry·Henry Kwok, Patrick W H Cheung
Oct 3, 2007·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·David H Ledbetter, Christa Lese Martin
Apr 15, 2008·American Journal of Human Genetics·Rikke S MøllerVera M Kalscheuer
Dec 3, 2009·European Journal of Human Genetics : EJHG·Wei ChenHans-Hilger Ropers
Dec 25, 2009·Nature·Philip J StephensMichael R Stratton
Jan 12, 2010·Annual Review of Medicine·Paweł Stankiewicz, James R Lupski
Feb 5, 2011·Nature·Ryan E MillsUNKNOWN 1000 Genomes Project
Sep 16, 2011·Seizure : the Journal of the British Epilepsy Association·Francesco NicitaAlberto Spalice
Feb 1, 2012·Nature Methods·Monya Baker
Oct 10, 2014·Journal of Human Genetics·Toshifumi SuzukiNaomichi Matsumoto
Feb 17, 2015·Nature Methods·Miten JainMark Akeson
Oct 4, 2015·Nature·Peter H SudmantJan O Korbel
Jan 21, 2016·Cancer Biology & Therapy·Alexis L NorrisWinston Timp
Apr 14, 2016·Proceedings of the National Academy of Sciences of the United States of America·Francesca MenghiEdison T Liu
Jun 8, 2017·Neurology. Genetics·Michael AlberBerge A Minassian

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Citations

Nov 16, 2019·Nature Reviews. Genetics·Steve S HoRyan E Mills
Apr 26, 2019·Journal of Thrombosis and Haemostasis : JTH·Nicolas ChatronYohann Jourdy
Sep 29, 2019·Journal of Human Genetics·Satomi Mitsuhashi, Naomichi Matsumoto
May 28, 2019·Frontiers in Genetics·Tuomo MantereAlexander Hoischen
Jun 7, 2020·Nature Reviews. Genetics·Glennis A LogsdonEvan E Eichler

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