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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

Abstract: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.

Otras publicaciones de la misma revista o congreso con autores/as de la Universidad de Cantabria

 Fuente: Genome Biol. 2014 Mar 25;15(3):R53

Editorial: BIOMED CENTRAL LTD

 Fecha de publicación: 25/03/2014

Nº de páginas: 18

Tipo de publicación: Artículo de Revista

 DOI: 10.1186/gb-2014-15-3-r53.

ISSN: 1474-760X,1474-7596,1465-6906

Autores/as

BROWNSTEIN, CATHERINE A.

BEGGS, ALAN H.

HOMER, NILS

MERRIMAN, BARRY

YU, TIMOTHY W.

FLANNERY, KATHERINE C.

DECHENE, ELIZABETH T.

TOWNE, MEGHAN C.

SAVAGE, SARAH K.

PRICE, EMILY N.

HOLM, INGRID A.

LUQUETTE, LOVELACE J.

LYON, ELAINE

MAJZOUB, JOSEPH

NEUPERT, PETER

MCCALLIE, DAVID JR.

SZOLOVITS, PETER

WILLARD, HUNTINGTON F.

MENDELSOHN, NANCY J.

TEMME, RENEE

FINKEL, RICHARD S.

YUM, SABRINA W.

MEDNE, LIVIJA

SUNYAEV, SHAMIL R.

ADZHUBEY, IVAN

CASSA, CHRISTOPHER A.

BAKKER, PAUL IW DE

DUZKALE, HATICE

DWORZYÑSKI, PIOTR

FAIRBROTHER, WILLIAM

FRANCIOLI, LAURENT

FUNKE, BIRGIT H.

GIOVANNI, MONICA A.

HANDSAKER, ROBERT E.

LAGE, KASPER

LEBO, MATTHEW S.

LEK, MONKOL

LESHCHINER, IGNATY

MACARTHUR, DANIEL G.

MCLAUGHLIN, HEATHER M.

MURRAY, MICHAEL F.

PERS, TUNE H.

POLAK, PAZ P.

RAYCHAUDHURI, SOUMYA

REHM, HEIDI L.

SOEMEDI, RACHEL

STITZIEL, NATHAN O.

VESTECKA, SARA

SUPPER, JOCHEN

GUGENMUS, CLAUDIA

KLOCKE, BERNWARD

HAHN, ALEXANDER

SCHUBACH, MAX

MENZEL, MORTIZ

BISKUP, SASKIA

FREISINGER, PETER

DENG, MARIO

BRAUN, MARTIN

PERNER, SVEN

SMITH, RICHARD J.H.

ANDORF, JANEEN L.

HUANG, JIAN

RYCKMAN, KELLI

SHEFFIELD, VAL C.

STONE, EDWIN M.

BAIR, THOMAS

BLACK-ZIEGELBEIN, E. ANN

BRAUN, TERRY A.

DARBRO, BENJAMIN

DELUCA, ADAM P.

KOLBE, DIANA L.

SCHEETZ, TODD E.

SHEARER, AIDEN E.

SOMPALLAE, RAMA

WANG, KAI

BASSUK, ALEXANDER G.

EDENS, ERIK

MATHEWS, KATHERINE

MOORE, STEVEN A.

SHCHELOCHKOV, OLEG A.

TRAPANE, PAMELA

BOSSLER, AARON

CAMPBELL, COLLEEN A.

HEUSEL, JONATHAN W.

KWITEK, ANNE

MAGA, TARA

PANZER, KARIN

WASSINK, THOMAS

DAELE, DOUGLAS VAN

AZAIEZ, HELA

BOOTH, KEVIN

MEYER, NIC

SEGAL, MICHAEL M.

WILLIAMS, MARC S.

TROMP, GERARD

WHITE, PETER

CORSMEIER, DONALD

FITZGERALD-BUTT, SARA

HERMAN, GAIL

LAMB-THRUSH, DEVON

MCBRIDE, KIM L.

NEWSOM, DAVID

PIERSON, CHRISTOPHER R.

RAKOWSKY, ALEXANDER T.

MAVER, ALES

LOVRECIC, LUCA

PALANDACIC, ANJA

PETERLIN, BORUT

TORKAMANI, ALI

WEDELL, ANNA

HUSS, MIKAEL

ALEXEYENKO, ANDREY

LINDVALL, JESSICA M.

MAGNUSSON, MANS

NILSSON, DANIEL

STRANNEHEIM, HENRIK

TAYLAN, FULYA

GILISSEN, CHRISTIAN

HOISCHEN, ALEXANDER

BON, BREGJE VAN

YNTEMA, HELGER

NELEN, MARCEL

ZHANG, WEIDONG

SAGER, JASON

ZHANG, LU

BLAIR, KATHRYN

KURAL, DENIZ

CARIASO, MICHAEL

LENNON, GREG G.

JAVED, ASIF

AGRAWAL, SALONI

NG, PAULINE C.

SANDHU, KOMAL S.

KRISHNA, SHUBA

VEERAMACHANENI, VAMSI

ISAKOV, OFER

HALPERIN, ERAN

FRIEDMAN, EITAN

SHOMRON, NOAM

GLUSMAN, GUSTAVO

ROACH, JARED C.

CABALLERO, JUAN

COX, HANNAH C.

MAULDIN, DENISE

AMENT, SETH A.

ROWEN, LEE

RICHARDS, DANIEL R.

LUCAS, F. ANTHONY SAN

GONZALEZ GARAY, MANUEL L.

CASKEY, C. THOMAS

BAI, YU

HUANG, YING

FANG, FANG

ZHANG, YAN

WANG, ZHENGYUAN

JORGE DE LA BARRERA MARTINEZ

REESE, MARTIN G.

VEGA, FRANCISCO M. DE LA

KIRULUTA, EDWARD

CARGILL, MICHELE

HART, REECE K.

SORENSON, JON M.

LYON, GHOLSON J.

STEVENSON, DAVID A.

BRAY, BRUCE E.

MOORE, BARRY M.

EILBECK, KAREN

YANDELL, MARK

ZHAO, HONGYU

HOU, LIN

CHEN, XIAOWEI

YAN, XITING

CHEN, MENGJIE

LI, CONG

YANG, CAN

GUNEL, MURAT

LI, PEINING

KONG, YONG

ALEXANDER, AUSTIN C.

ALBERTYN, ZAYED

BOYCOTT, KYM M.

BULMAN, DENNIS E.

GORDON, PAUL M.K.

INNES, A MICHEIL

KNOPPERS, BARTHA M.

MAJEWSKI, JACEK

MARSHALL, CHRISTIAN R.

PARBOOSINGH, JILLIAN S.

SAWYER, SARAH L.

SAMUELS, MARK E.

SCHWARTZENTRUBER, JEREMY

KOHANE, ISAAC S.

MARGULIES, DAVID M.