Clinical Exome Studies Have Inconsistent Coverage.
Exome sequencing has become a commonly used clinical diagnostic test. Multiple studies have examined the diagnostic utility and individual laboratory performance of exome testing; however, no previous study has surveyed and compared the data quality from multiple clinical laboratories. METHODS: We e...
| Publicado en: | Clinical Chemistry Vol. 66; no. 1; pp. 199 - 207 |
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| Autores principales: | , , , , , , , , , , , , |
| Formato: | Journal Article |
| Publicado: |
Oxford University Press / USA
Jan2020
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=145704319&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 145704319 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00099147 10CS jtl: Clinical Chemistry issn: 00099147 maglogo: N pubinfo: dt: Jan2020 vid: 66 iid: 1 pid: 622 pub: Oxford University Press / USA artinfo: ui: 145704319 10.1093/clinchem.2019.306795 145704319 ppf: 199 ppct: 8 formats: fmt: @attributes: type: P tig: atl: Clinical Exome Studies Have Inconsistent Coverage. aug: au: Gotway, Garrett Crossley, Eric Kozlitina, Julia Chao Xing Fan, Judy Hornbuckle, Callie Thies, Jenny Michel, Donnice Quinn, Christine Scheuerle, Angela E. Umana, Luis A. Uhles, Crescenda L. Park, Jason Y. affil: McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX. sug: ab: Exome sequencing has become a commonly used clinical diagnostic test. Multiple studies have examined the diagnostic utility and individual laboratory performance of exome testing; however, no previous study has surveyed and compared the data quality from multiple clinical laboratories. METHODS: We examined sequencing data from 36 clinical exome tests from 3 clinical laboratories. Exome data were compared in terms of overall characteristics and coverage of specific genes and nucleotide positions. The sets of genes examined included genes in Consensus Coding Sequence (CCDS) (n 17 723), a subset of genes clinically relevant to epilepsy (n 108), and genes that are recommended for reporting of secondary findings (n 57; excludes X-linked genes). RESULTS: The average exome nucleotide coverage (20) of each laboratory varied at 96.49% (CV 3%), 96.54% (CV1%), and 91.68% (CV4%), for laboratories A, B, and C, respectively. For CCDS genes, the average number of completely covered genes varied at 12184 (CV 29%), 11687 (CV 13%), and 5989 (CV 37%), for laboratories A, B, and C, respectively. With smaller subsets of genes related to epilepsy and secondary findings, the CV revealed low consistency, with a maximum CV seen in laboratory C for both epilepsy genes (CV 60%) and secondary findings genes (CV 71%). CONCLUSIONS: Poor consistency in complete gene coverage was seen in the clinical exomelaboratories surveyed. The degree of consistency varied widely between the laboratories. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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