AMYCNE: Confident copy number assessment using whole genome sequencing data

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Fältnamn	Indikatorer	Metadata
000		03634naa a2200361 4500
001		oai:gup.ub.gu.se/266259
003		SwePub
008		240528s2018 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
009		oai:prod.swepub.kib.ki.se:138122038
024	7	a https://gup.ub.gu.se/publication/2662592 URI
024	7	a https://doi.org/10.1371/journal.pone.01897102 DOI
024	7	a http://kipublications.ki.se/Default.aspx?queryparsed=id:1381220382 URI
040		a (SwePub)gud (SwePub)ki
041		a eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Eisfeldt, J.u Karolinska Institutet4 aut
245	1 0	a AMYCNE: Confident copy number assessment using whole genome sequencing data
264		c 2018-03-26
264	1	b Public Library of Science (PLoS),c 2018
520		a Copy number variations (CNVs) within the human genome have been linked to a diversity of inherited diseases and phenotypic traits. The currently used methodology to measure copy numbers has limited resolution and/or precision, especially for regions with more than 4 copies. Whole genome sequencing (WGS) offers an alternative data source to allow for the detection and characterization of the copy number across different genomic regions in a single experiment. A plethora of tools have been developed to utilize WGS data for CNV detection. None of these tools are designed specifically to accurately estimate copy numbers of complex regions in a small cohort or clinical setting. Herein, we present AMYCNE (automatic modeling functionality for copy number estimation), a CNV analysis tool using WGS data. AMYCNE is multifunctional and performs copy number estimation of complex regions, annotation of VCF files, and CNV detection on individual samples. The performance of AMYCNE was evaluated using AMY1A ddPCR measurements from 86 unrelated individuals. In addition, we validated the accuracy of AMYCNE copy number predictions on two additional genes (FCGR3A and FCGR3B) using datasets available through the 1000 genomes consortium. Finally, we simulated levels of mosaic loss and gain of chromosome X and used this dataset for benchmarking AMYCNE. The results show a high concordance between AMYCNE and ddPCR, validating the use of AMYCNE to measure tandem AMY1 repeats with high accuracy. This opens up new possibilities for the use of WGS for accurate copy number determination of other complex regions in the genome in small cohorts or single individuals. © 2018 Eisfeldt et al.
650	7	a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe
650	7	a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng
700	1	a Nilsson, D.u Karolinska Institutet4 aut
700	1	a Andersson-Assarsson, Johanna C.,d 1974u Gothenburg University,Göteborgs universitet,Institutionen för medicin, avdelningen för molekylär och klinisk medicin,Institute of Medicine, Department of Molecular and Clinical Medicine4 aut0 (Swepub:gu)xanjoh
700	1	a Lindstrand, A.u Karolinska Institutet4 aut
710	2	a Karolinska Institutetb Institutionen för medicin, avdelningen för molekylär och klinisk medicin4 org
773	0	t Plos Oned : Public Library of Science (PLoS)g 13:3q 13:3x 1932-6203
856	4	u https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0189710&type=printable
856	4 8	u https://gup.ub.gu.se/publication/266259
856	4 8	u https://doi.org/10.1371/journal.pone.0189710
856	4 8	u http://kipublications.ki.se/Default.aspx?queryparsed=id:138122038

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Av författaren/redakt...: Eisfeldt, J.; Nilsson, D.; Andersson-Assars ...; Lindstrand, A.

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MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Medicinsk geneti ...

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