scholarly journals Integrated Protein Network Analysis of Whole Exome Sequencing Study of Severe Preeclampsia

2020 ◽  
Author(s):  
Jessica Schuster ◽  
George A. Tollefson ◽  
Valeria Zarate ◽  
Anthony Agudelo ◽  
Joan Stabila ◽  
...  
Keyword(s):  
Network Analysis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Severe Preeclampsia ◽  
Risk Scores ◽  
Whole Exome ◽  
Cluster A ◽  
Shared Networks ◽  
Unique Genes

AbstractTo identify clusters of patients with shared networks of genes associated with early onset severe preeclampsia from whole exome sequencing data through novel bioinformatic analysis.We performed a case-control study using whole exome sequencing (WES) on early onset preeclamptic mothers with severe features delivering < 34 weeks and mothers who delivered ≥ 37 weeks. Genotype testing identified variants that were differentially abundant between cases and controls. A Protein-Protein interaction (PPI) analysis and visualization tool, Proteinarium, was implemented to identify clusters of patients with shared networks associated with severe preeclampsia.A total of 61 early onset preeclamptic women with severe features and 82 race and ethnicity matched control women at term were sequenced. We identified 8,867 predicted deleterious variants. 21 of these variants were nominally associated with preeclampsia by genotype testing. Using Proteinarium129 out of the 143 sequenced patients were assigned to statistically significant clusters, Cluster A and B (p< 0.0001). Case dominated Cluster A contained 47 of the 61 case subjects. There were 13 unique genes in the PPI network of Cluster A compared to control dominated Cluster B. Amongst these unique genes, LAMB2, PTK2, RAC1, QSOX1, FN1, and VCAM1 have known associations with the pathogenic mechanisms of preeclampsia.Our network analysis identified genes that were unique to a large cluster of patients with shared networks that provide insights for severe preeclampsia. We also identified genes imputed from the interactome that may otherwise have not been identified by conventional analysis. Strict phenotyping of both cases and controls improved the likelihood of identifying these otherwise difficult to find genetic associations. These uniquely identified genes and their associated variants are potential candidates for developing polygenic risk scores for severe preeclampsia. These results support our hypothesis on the genetic architecture of complex diseases and are generalizable to other phenotypes.

scholarly journals Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons

2015 ◽  
Vol 24 (5) ◽  
pp. 710-716 ◽  
Author(s):  
Gaël Nicolas ◽  
David Wallon ◽  
Camille Charbonnier ◽  
Olivier Quenez ◽  
Stéphane Rousseau ◽  
...  
Keyword(s):  
Alzheimer Disease ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Whole Exome

scholarly journals Early Onset Multiple Primary Tumors in Atypical Presentation of Cowden Syndrome Identified by Whole-Exome-Sequencing

2018 ◽  
Vol 9 ◽  
Author(s):  
Mathias Cavaillé ◽  
Flora Ponelle-Chachuat ◽  
Nancy Uhrhammer ◽  
Sandrine Viala ◽  
Mathilde Gay-Bellile ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Cowden Syndrome ◽  
Atypical Presentation ◽  
Primary Tumors ◽  
Multiple Primary Tumors ◽  
Whole Exome ◽  
Multiple Primary

scholarly journals CARMIL2 Deficiency Presenting as Very Early Onset Inflammatory Bowel Disease

2019 ◽  
Vol 25 (11) ◽  
pp. 1788-1795 ◽  
Author(s):  
Thomas Magg ◽  
Anna Shcherbina ◽  
Duran Arslan ◽  
Mukesh M Desai ◽  
Sarah Wall ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Mononuclear Cells ◽  
Severe Disease ◽  
Effector Memory ◽  
Loss Of Function ◽  
Peripheral Blood Mononuclear ◽  
Whole Exome ◽  
Inflammatory Bowel

Abstract Background Children with very early onset inflammatory bowel diseases (VEO-IBD) often have a refractory and severe disease course. A significant number of described VEO-IBD-causing monogenic disorders can be attributed to defects in immune-related genes. The diagnosis of the underlying primary immunodeficiency (PID) often has critical implications for the treatment of patients with IBD-like phenotypes. Methods To identify the molecular etiology in 5 patients from 3 unrelated kindred with IBD-like symptoms, we conducted whole exome sequencing. Immune workup confirmed an underlying PID. Results Whole exome sequencing revealed 3 novel CARMIL2 loss-of-function mutations in our patients. Immunophenotyping of peripheral blood mononuclear cells showed reduction of regulatory and effector memory T cells and impaired B cell class switching. The T cell proliferation and activation assays confirmed defective responses to CD28 costimulation, consistent with CARMIL2 deficiency. Conclusion Our study highlights that human CARMIL2 deficiency can manifest with IBD-like symptoms. This example illustrates that early diagnosis of underlying PID is crucial for the treatment and prognosis of children with VEO-IBD.

scholarly journals Whole exome sequencing identifies FBN1 mutations in two patients with early-onset type B aortic dissection

2017 ◽  
Vol 16 (5) ◽  
pp. 6620-6625
Author(s):  
Qian Han ◽  
Wenwen Zhang ◽  
Changjian Liu ◽  
Min Zhou ◽  
Feng Ran ◽  
...  
Keyword(s):  
Aortic Dissection ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Type B ◽  
Type B Aortic Dissection ◽  
Onset Type ◽  
Whole Exome

P2-131: WHOLE-EXOME SEQUENCING OF HISPANIC EARLY-ONSET ALZHEIMER DISEASE FAMILIES IDENTIFIES RARE VARIANTS IN MULTIPLE ALZHEIMER'S-RELATED GENES

2014 ◽  
Vol 10 ◽  
pp. P518-P519
Author(s):  
Margaret Pericak-Vance ◽  
Christiane Reitz ◽  
Brian W. Kunkle ◽  
Badri N. Vardarajan ◽  
Martin A. Kohli ◽  
...  
Keyword(s):  
Alzheimer Disease ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Rare Variants ◽  
Whole Exome

scholarly journals Whole-exome sequencing reveals an inherited R566X mutation of the epithelial sodium channel β-subunit in a case of early-onset phenotype of Liddle syndrome

2016 ◽  
Vol 2 (6) ◽  
pp. a001255 ◽  
Author(s):  
Linda M. Polfus ◽  
Eric Boerwinkle ◽  
Richard A. Gibbs ◽  
Ginger Metcalf ◽  
Donna Muzny ◽  
...  
Keyword(s):  
Sodium Channel ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Epithelial Sodium Channel ◽  
Β Subunit ◽  
Liddle Syndrome ◽  
Whole Exome

Variable penetrance of CDH1 mutation diffuse gastric cancer: A genomic analysis.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 4082-4082
Author(s):  
David Paul Kelsen ◽  
Kasmintan A. Schrader ◽  
Raya Khanin ◽  
Laura H. Tang ◽  
Erin E. Salo-Mullen ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Germ Line ◽  
Diffuse Gastric Cancer ◽  
Second Hit ◽  
Whole Exome ◽  
Prophylactic Gastrectomy ◽  
Variable Penetrance

4082 Background: CDH1 encodes E-cadherin; mutations (CDH1mut) increase the risk of diffuse gastric (DGC) and lobular breast cancers. Life-time risk of DGC is estimated at 80%. Current recommendations are prophylactic gastrectomy (PG) in CDH1mut carriers after age 20. Foci of DGC are found in some PG; others have none at PG, and some CDH1mut without PG never develop cancer. Identifying risk modifying alleles or other genomic events which increase the risk of DGC may improve understanding of DGC and may provide a biomarker for when to perform PG. Methods: For a Gastric Cancer Registry, we collected family pedigrees, germline DNA and FFPE tumor from CDH1mut DGC patients (pts) and their families. From 24 families, with 52 CDH1mut individuals, we identified 4 families in which a young CDH1mut pt developed advanced DGC while their CDH1mut parent and siblings had no clinical evidence of DGC. Several relatives had undergone PG with no DGC found. We hypothesize that there are risk modifying alleles and/or a “second hit” that causes variable penetrance and early onset of DGC in the young CDH1mut pts. Whole genome sequencing was performed on germ line DNA (Complete Genomics, Inc. Mountain View, CA); and whole exome sequencing on tumor specimens (MSKCC). Results: To date, 4 DGC pts and 8 relatives from 4 families have been studied. All 4 affected pts were women (ages 17, 25, 27, 42); their unaffected CDH1mut parents were 41, 51, 54, and 70 years old. The families are of Kenyan, Scandinavian, Italian, Eastern European, and Scottish origin. CDH1 mutations for the pts and their families were confirmed on WGS, and were as follows: 1451C>A(pro484his);c. 1792C>T (arg598ter);c. 1893dupA in exon 12;c. 1565+1G>A (IVS10+1G>A). Analysis of germline DNA for modifying alleles is being performed (Ingenuity Systems, Redwood, Ca.); whole exome sequencing of tumor to identify a possible "second hit" is underway. These data will be presented. Conclusions: Since at least some older pts with proven CDH-1mut do not develop DGC while their children do, CGH-1mut alone may not be sufficient to cause early onset DGC. We hope to identify the additional genomic events associated with early onset advanced DGC. Supported in part by grants from the Gerstner and DeGregorio Foundations.

scholarly journals Whole-Exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity

Obesity ◽  
2013 ◽  
Vol 22 (2) ◽  
pp. 576-584 ◽  
Author(s):  
Richard Gill ◽  
Yee Him Cheung ◽  
Yufeng Shen ◽  
Patricia Lanzano ◽  
Nazrat M. Mirza ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Whole Exome
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