title: Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.
abstract: With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of "next-generation cytogenetics" (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013). This system starts with the alignment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and detailed description of chromosomal changes. To facilitate usage and implementation of this nomenclature, we are developing a program designated BLA(S)T Output Sequence Tool of Nomenclature (BOSToN), a demonstrative version of which is accessible online. A standardized characterization of structural chromosomal rearrangements is essential both for research analyses and for application in the clinical setting.
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Zehra
authors.initials: Z
authors.lastname: Ordulu
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Kristen E
authors.initials: KE
authors.lastname: Wong
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Benjamin B
authors.initials: BB
authors.lastname: Currall
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Ivanov
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Shahrin
authors.initials: S
authors.lastname: Pereira
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Althari
authors.affiliation: Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: James F
authors.initials: JF
authors.lastname: Gusella
authors.affiliation: Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Talkowski
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address: cmorton@partners.org.
authors.forename: Cynthia C
authors.initials: CC
authors.lastname: Morton
mesh_terms: D001483:Base Sequence; D002869:Chromosome Aberrations / Q000145:classification*; D020732:Cytogenetic Analysis / Q000145:classification*; D004252:DNA Mutational Analysis; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D012984:Software; D009626:Terminology as Topic
references.citation: Nature. 2009 Dec 24;462(7276):1005-10
references.pmid: 20033038
references.citation: Cytogenet Cell Genet. 1981;31(1):5-23
references.pmid: 7297128
references.citation: Exp Cell Res. 1968 Jan;49(1):219-22
references.pmid: 5640698
references.citation: Eur J Hum Genet. 2014 May;22(5):652-9
references.pmid: 24105367
references.citation: Genet Med. 2013 Sep;15(9):733-47
references.pmid: 23887774
references.citation: Cytogenet Cell Genet. 1978;21(6):309-409
references.pmid: 747930
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Birth Defects Orig Artic Ser. 1985;21(1):1-117
references.pmid: 4041569
references.citation: Nat Genet. 2012 Mar 04;44(4):390-7, S1
references.pmid: 22388000
references.citation: Hereditas. 1972;67(1):147-9
references.pmid: 4142004
references.citation: N Engl J Med. 2012 Dec 6;367(23):2226-32
references.pmid: 23215558
references.citation: Am J Med Genet A. 2014 Feb;164A(2):377-85
references.pmid: 24311194
references.citation: Nature. 2010 Oct 28;467(7319):1109-13
references.pmid: 20981101
references.citation: Genet Med. 2013 Jun;15(6):484-94
references.pmid: 23619274
references.citation: Am J Hum Genet. 2012 Dec 7;91(6):1128-34
references.pmid: 23217328
references.citation: Genet Med. 2011 Jul;13(7):676-9
references.pmid: 21681105
references.citation: Am J Hum Genet. 2009 Apr;84(4):524-33
references.pmid: 19344873
references.citation: Mol Oncol. 2013 Aug;7(4):743-55
references.pmid: 23769412
references.citation: Cell. 1984 Jun;37(2):511-20
references.pmid: 6327071
references.citation: Cell. 2011 Mar 4;144(5):646-74
references.pmid: 21376230
references.citation: J Med Genet. 2013 Mar;50(3):144-50
references.pmid: 23315544
references.citation: Cancer Lett. 2013 Nov 1;340(2):284-95
references.pmid: 23174106
references.citation: Hum Genet. 2013 May;132(5):537-52
references.pmid: 23354975
references.citation: Ann Hum Genet. 1960 Dec;24:319-25
references.pmid: 14447289
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D1027-32
references.pmid: 24253300
references.citation: Cell. 2012 Apr 27;149(3):525-37
references.pmid: 22521361
references.citation: EMBO J. 1983;2(12):2375-83
references.pmid: 6321164
references.citation: Cytogenetics. 1972;11(5):317-62
references.pmid: 4647417
references.citation: Genome Res. 2008 Jul;18(7):1143-9
references.pmid: 18326688
references.citation: Cell. 2011 Jan 7;144(1):27-40
references.pmid: 21215367
references.citation: Genome Res. 2002 Jun;12(6):996-1006
references.pmid: 12045153
references.citation: Nature. 2008 Nov 6;456(7218):53-9
references.pmid: 18987734
references.citation: Genet Med. 2013 Nov;15(11):901-9
references.pmid: 24071793
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9
references.pmid: 23155063
references.citation: Science. 2007 Oct 19;318(5849):420-6
references.pmid: 17901297
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D986-92
references.pmid: 24174537
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Am J Hum Genet. 2011 Apr 8;88(4):469-81
references.pmid: 21473983