Lessons learned from additional research analyses of unsolved clinical exome cases.
Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery.



We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols.



Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3).



An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN, 46202, USA.
Mohammad K
MK
Eldomery
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Zeynep
Z
Coban-Akdemir
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Tamar
T
Harel
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Jill A
JA
Rosenfeld
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland.
Tomasz
T
Gambin
Norwegian National Unit for Newborn Screening, Women and Children's Division, Oslo University Hospital, 0424, Oslo, Norway.
Asbjørg
A
Stray-Pedersen
CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1, France.
Sébastien
S
Küry
CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1, France.|Atlantic Gene Therapies, UMR1089, Nantes, France.
Sandra
S
Mercier
Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
Davor
D
Lessel
Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
Jonas
J
Denecke
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Wojciech
W
Wiszniewski
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Samantha
S
Penney
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Pengfei
P
Liu
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Weimin
W
Bi
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Seema R
SR
Lalani
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.|Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
Christian P
CP
Schaaf
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Michael F
MF
Wangler
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Carlos A
CA
Bacino
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
Richard Alan
RA
Lewis
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Lorraine
L
Potocki
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Brett H
BH
Graham
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
John W
JW
Belmont
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
Fernando
F
Scaglia
Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital Center for Human Immuno-Biology, Houston, TX, USA.
Jordan S
JS
Orange
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Shalini N
SN
Jhangiani
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Theodore
T
Chiang
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Harsha
H
Doddapaneni
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Jianhong
J
Hu
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Donna M
DM
Muzny
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Fan
F
Xia
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Arthur L
AL
Beaudet
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.|Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
Eric
E
Boerwinkle
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Christine M
CM
Eng
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.|Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, 7703, USA.
Sharon E
SE
Plon
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Texas Children's Hospital, Houston, TX, 77030, USA.
V Reid
VR
Sutton
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA.
Richard A
RA
Gibbs
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Jennifer E
JE
Posey
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.|Baylor Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Yaping
Y
Yang
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. jlupski@bcm.edu.|Texas Children's Hospital, Houston, TX, 77030, USA. jlupski@bcm.edu.|Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA. jlupski@bcm.edu.|Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. jlupski@bcm.edu.|Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA. jlupski@bcm.edu.
James R
JR
Lupski
D000074183:ATPases Associated with Diverse Cellular Activities; D000251:Adenosine Triphosphatases / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D004268:DNA-Binding Proteins / Q000235:genetics; D059472:Exome; D005260:Female; D044387:GTP-Binding Protein beta Subunits / Q000235:genetics; D030342:Genetic Diseases, Inborn / Q000175:diagnosis* / Q000235:genetics / Q000378:metabolism; D023281:Genomics / Q000379:methods*; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D008666:Metalloendopeptidases / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics
C549686:ATAD3A protein, human; D004268:DNA-Binding Proteins; C490611:GNB5 protein, human; D044387:GTP-Binding Protein beta Subunits; D008565:Membrane Proteins; D024101:Mitochondrial Proteins; C501130:PURA protein, human; D014157:Transcription Factors; D008666:Metalloendopeptidases; C068038:mitochondrial intermediate peptidase; D000251:Adenosine Triphosphatases; D000074183:ATPases Associated with Diverse Cellular Activities