A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.
While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation, and reporting of clinically significant variants. This study aimed to examine the workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization.



Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free-text responses that were later clarified with phone interviews.



Twenty-one laboratories participated. Practices highly concordant across all groups included consent documentation, multiperson case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing, or patient access to data.



This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas of development in best practice guidelines that may be helpful.Genet Med advance online publication 03 Novemeber 2016.
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Julianne M
0000-0001-5843-4432
JM
O'Daniel
Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.
Heather M
HM
McLaughlin
Division of Medical Genetics, University of Washington, Seattle, Washington, USA.
Laura M
0000-0002-5506-6168
LM
Amendola
GeneDx, Inc., Gaithersburg, Maryland, USA.
Sherri J
SJ
Bale
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Jonathan S
0000-0003-2360-2664
JS
Berg
Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
David
0000-0002-8750-306X
D
Bick
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Kevin M
KM
Bowling
Ambry Genetics, Aliso Viejo, California, USA.|Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, California, USA.
Elizabeth C
EC
Chao
Department of Pediatrics, Columbia University, New York, New York, USA.|Department of Medicine, Columbia University, New York, New York, USA.
Wendy K
0000-0003-3438-5685
WK
Chung
Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Laura K
0000-0003-2330-8158
LK
Conlin
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Gregory M
GM
Cooper
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
Soma
S
Das
Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
Joshua L
0000-0003-3587-830X
JL
Deignan
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Michael O
MO
Dorschner
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
James P
JP
Evans
Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA.
Arezou A
0000-0002-4439-8554
AA
Ghazani
Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA.
Katrina A
0000-0001-9535-8993
KA
Goddard
Department of Internal Medicine, Center for Bioethics Social Science and Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Michele
0000-0002-3451-8858
M
Gornick
Ambry Genetics, Aliso Viejo, California, USA.
Kelly D
0000-0003-1173-052X
KD
Farwell Hagman
Illumina, Inc., San Diego, California, USA.
Tina
T
Hambuch
Emory Genetics Laboratory, Department of Human Genetics, Emory University, Atlanta, Georgia, USA.
Madhuri
M
Hegde
Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland, USA.
Lucia A
LA
Hindorff
Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, Massachusetts, USA.|Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.
Ingrid A
IA
Holm
Division of Medical Genetics, University of Washington, Seattle, Washington, USA.|Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Gail P
GP
Jarvik
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
Amy
A
Knight Johnson
Emory Genetics Laboratory, Department of Human Genetics, Emory University, Atlanta, Georgia, USA.
Lindsey
L
Mighion
Personalis, Inc., Menlo Park, California, USA.
Massimo
M
Morra
Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.
Sharon E
0000-0002-9626-0936
SE
Plon
Department of Molecular and Medical Genetics, Oregon Health &Science University, Portland, Oregon, USA.
Sumit
0000-0002-2274-8218
S
Punj
Department of Molecular and Medical Genetics, Oregon Health &Science University, Portland, Oregon, USA.
C Sue
0000-0003-1078-979X
CS
Richards
Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Avni
0000-0003-2871-4307
A
Santani
Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Brian H
BH
Shirts
Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Nancy B
0000-0001-8109-3648
NB
Spinner
Ambry Genetics, Aliso Viejo, California, USA.
Sha
0000-0002-8304-2286
S
Tang
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.|Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Karen E
KE
Weck
Consortium on Law and Values in Health, Environment &the Life Sciences, Law School, Medical School, University of Minnesota, Minneapolis, Minnesota, USA.
Susan M
SM
Wolf
Department of Molecular and Human Genetics, Baylor College of Medicine and Baylor Miraca Genetics Laboratories, Houston, Texas, USA.
Yaping
0000-0001-5608-8628
Y
Yang
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Department of Pathology, Brigham &Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
Heidi L
0000-0002-6025-0015
HL
Rehm
D030881:Disclosure; D005820:Genetic Testing / Q000379:methods* / Q000592:standards; D006801:Humans; D033162:Incidental Findings; D033181:Information Dissemination; D007753:Laboratories / Q000941:ethics / Q000592:standards*; D017410:Practice Guidelines as Topic; D058028:Research Report; D018401:Sample Size; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D011795:Surveys and Questionnaires