A pipeline for complete characterization of complex germline rearrangements from long DNA reads

[1]  M. Frith,et al.  Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer–Giedion syndrome and Cornelia de Lange syndrome-4 , 2020, Journal of Human Genetics.

[2]  M. Frith,et al.  Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease , 2019, Nature Genetics.

[3]  Leon Di Stefano,et al.  Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software , 2019, Nature Communications.

[4]  C. Shaw,et al.  Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 , 2019, Cell.

[5]  F. Vezzi,et al.  Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements , 2019, PLoS genetics.

[6]  Evan E. Eichler,et al.  Characterizing the Major Structural Variant Alleles of the Human Genome , 2019, Cell.

[7]  Andrew R. Webster,et al.  Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing , 2018, Genome Medicine.

[8]  Martin C Frith,et al.  A survey of localized sequence rearrangements in human DNA , 2017, Nucleic acids research.

[9]  R. Shamir,et al.  Reconstructing cancer karyotypes from short read data: the half empty and half full glass , 2017, BMC Bioinformatics.

[10]  G. Lunter,et al.  A high throughput screen for active human transposable elements , 2017, BMC Genomics.

[11]  Michael C. Schatz,et al.  Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.

[12]  B. Schmidt,et al.  CLOVE: classification of genomic fusions into structural variation events , 2017, BMC Bioinformatics.

[13]  Tam P. Sneddon,et al.  Long-read genome sequencing identifies causal structural variation in a Mendelian disease , 2017, Genetics in Medicine.

[14]  Edwin Cuppen,et al.  Mapping and phasing of structural variation in patient genomes using nanopore sequencing , 2017, Nature Communications.

[15]  Ryan L. Collins,et al.  Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome , 2017, Genome Biology.

[16]  Kiyoshi Asai,et al.  Training alignment parameters for arbitrary sequencers with LAST-TRAIN , 2016, Bioinform..

[17]  J. Kidd,et al.  Discovery of unfixed endogenous retrovirus insertions in diverse human populations , 2016, Proceedings of the National Academy of Sciences.

[18]  Gabor T. Marth,et al.  An integrated map of structural variation in 2,504 human genomes , 2015, Nature.

[19]  M. Frith,et al.  Split-alignment of genomes finds orthologies more accurately , 2015, Genome Biology.

[20]  Satoru Miyano,et al.  Inferring the global structure of chromosomes from structural variations , 2015, BMC Genomics.

[21]  Naomichi Matsumoto,et al.  Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing , 2014, Journal of Human Genetics.

[22]  Alexander Kanapin,et al.  Unfixed Endogenous Retroviral Insertions in the Human Population , 2014, Journal of Virology.

[23]  Li Ding,et al.  Retrotransposition of gene transcripts leads to structural variation in mammalian genomes , 2013, Genome Biology.

[24]  M. Frith,et al.  Mammalian NUMT insertion is non-random , 2012, Nucleic acids research.

[25]  Markus J. van Roosmalen,et al.  Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. , 2012, Cell reports.

[26]  Benjamin J. Raphael,et al.  Reconstructing cancer genomes from paired-end sequencing data , 2012, BMC Bioinformatics.

[27]  H. Kazazian,et al.  Pathogenic orphan transduction created by a nonreference LINE‐1 retrotransposon , 2012, Human mutation.

[28]  N. Matsumoto,et al.  Early infantile epileptic encephalopathy associated with the disrupted gene encoding Slit‐Robo Rho GTPase activating protein 2 (SRGAP2) , 2012, American journal of medical genetics. Part A.

[29]  Adrian M. Stütz,et al.  A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans , 2011, PLoS genetics.

[30]  Markus J. van Roosmalen,et al.  Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. , 2011, Human molecular genetics.

[31]  Y. Fukushima,et al.  Breakpoint determination of X;autosome balanced translocations in four patients with premature ovarian failure , 2011, Journal of Human Genetics.

[32]  J. Lupski,et al.  Mechanisms of change in gene copy number , 2009, Nature Reviews Genetics.

[33]  N. Matsumoto,et al.  Characterization of the complex 7q21.3 rearrangement in a patient with bilateral split‐foot malformation and hearing loss , 2009, American journal of medical genetics. Part A.

[34]  S. Nussey,et al.  The association of primary hyperparathyroidism and primary ovarian failure: a de novo t(X; 2) (q22p13) reciprocal translocation. , 2008, European journal of endocrinology.

[35]  L. Symington,et al.  Template switching during break-induced replication , 2007, Nature.

[36]  Ryan E. Mills,et al.  Which transposable elements are active in the human genome? , 2007, Trends in genetics : TIG.

[37]  N. Niikawa,et al.  Subtelomere specific microarray based comparative genomic hybridisation: a rapid detection system for cryptic rearrangements in idiopathic mental retardation , 2004, Journal of Medical Genetics.

[38]  W S Watkins,et al.  Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. , 2001, Journal of molecular biology.

[39]  Kazutaka Katoh,et al.  lamassemble: Multiple Alignment and Consensus Sequence of Long Reads. , 2021, Methods in molecular biology.

[40]  J. V. Moran,et al.  The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes , 2015, Microbiology spectrum.

[41]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..