Evidence map›Paper›PMID 23830146›Full record

ArticleThe Journal of allergy and clinical immunology2013

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.

Rui Chen, Silvia Giliani, Gaetana Lanzi, George I Mias, Silvia Lonardi, Kerry Dobbs, John Manis, Hogune Im, Jennifer E Gallagher, Douglas H Phanstiel and 21 more

Open access · bronzeAbstract read
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Article in The Journal of allergy and clinical immunology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
85citing papers in PubMed, 1 pooled it
13.4field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

85 citing papers in PubMed, 1 synthesis or guideline pooled it, 159 citations in OpenAlex.

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25 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

31 authors at 10 institutions in 3 countries.

Rui ChenDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Silvia GilianiA. Nocivelli Institute for Molecular Medicine, Pediatric Clinic, University of Brescia, and the Section of Genetics, Department of Pathology Spedali Civili, Brescia, Italy.
Gaetana LanziA. Nocivelli Institute for Molecular Medicine, Pediatric Clinic, University of Brescia, and the Section of Genetics, Department of Pathology Spedali Civili, Brescia, Italy.
George I MiasDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Silvia LonardiDepartment of Pathology, University of Brescia, Brescia, Italy.
Kerry DobbsDivision of Immunology, Boston Children's Hospital, Harvard Medical School, Harvard Stem Cell Institute, Boston, Mass.
John ManisDepartment of Transfusion Medicine, Boston Children's Hospital, Boston, Mass.
Hogune ImDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Jennifer E GallagherDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Douglas H PhanstielDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Ghia EuskirchenDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Philippe LacrouteDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Keith BettingerDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif.
Daniele MorattoA. Nocivelli Institute for Molecular Medicine, Pediatric Clinic, University of Brescia, and the Section of Genetics, Department of Pathology Spedali Civili, Brescia, Italy.
Katja WeinachtDivision of Hematology and Oncology, Boston Children's Hospital, Boston, Mass.
Davide MontinDepartment of Public Health and Pediatrics, University of Torino, Torino, Italy.
Eleonora GalloDepartment of Public Health and Pediatrics, University of Torino, Torino, Italy.
Giovanna MangiliUSC Patologia Neonatale, Ospedali Riuniti di Bergamo, Bergamo, Italy.
Fulvio PortaDivision of Pediatric Hematology-Oncology, Spedali Civili Brescia, Brescia, Italy.
Lucia D NotarangeloDivision of Pediatric Hematology-Oncology, Spedali Civili Brescia, Brescia, Italy.
Stefania PedrettiUSC Patologia Neonatale, Ospedali Riuniti di Bergamo, Bergamo, Italy.
Waleed Al-HerzDepartment of Pediatrics, Al-Sabah Hospital, Kuwait City, Kuwait.
Wasmi AlfahdliDepartment of Surgery, Ibn-Sina Hospital, Kuwait City, Kuwait.
Anne Marie ComeauNew England Newborn Screening Program, University of Massachusetts Medical School, Worcester, Mass.
Russell S TraisterDepartment of Internal Medicine, Children's Hospital of Pittsburgh, Pittsburgh, Pa.
Sung-Yun PaiDivision of Hematology-Oncology, Boston Children's Hospital, Boston, Mass.
Graziella CarellaClinical Immunology and Allergology, Spedali Civili Brescia, Brescia, Italy.
Fabio FacchettiDepartment of Pathology, University of Brescia, Brescia, Italy.
Kari C NadeauDepartment of Pediatrics, Stanford University School of Medicine, Stanford, Calif. Electronic address: knadeau@stanford.edu.
Michael SnyderDepartment of Genetics, Stanford University School of Medicine, Stanford, Calif. Electronic address: mpsnyder@stanford.edu.
Luigi D NotarangeloDivision of Immunology, Boston Children's Hospital, Harvard Medical School, Harvard Stem Cell Institute, Boston, Mass; Harvard Stem Cell Institute, Harvard Medical School, Boston, Mass. Electronic address: Luigi.Notarangelo@childrens.harvard.edu.
Stanford University · USUniversity of Brescia · ITAzienda Socio Sanitaria Territoriale degli Spedali Civili di Brescia · ITBoston Children's Hospital · USUniversity of Bergamo · ITAl-Sabah Hospital · KWChildren's Hospital of Pittsburgh · USHarvard Stem Cell Institute · USIbn Sina Hospital · KWUniversity of Massachusetts Chan Medical School · US

Funding

INSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2M
Training of Clinical Investigators in Primary Immune DeficienciesU54AI082973 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI PUCK, JENNIFER M. · 2009 to 2023
$23.3M
Role of TACI mutations in CVIDP01AI076210 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI ALT, FREDERICK W. · 2009 to 2013
$9.0M
Genomics of Gene Regulation in Progenitor to Differentiated KeratinocytesU01HG007919 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2015 to 2017
$7.0M
Modeling and correcting human SCID using patient-derived iPS cellsR01AI100887 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI MANIS, JOHN P · 2012 to 2020
$4.5M
Role of HIV Envelope Proteins In Viral Replication and HIV PathogenesisZ01AI000887 · NIAID · NIAID EXTRAMURAL ACTIVITIES · PI FAUCI, ANTHONY S. · 2001 to 2008
$1.6M
Integrative Dynamic Omics Profiling: A First Step Towards Personalized MedicineR00HG007065 · NHGRI · MICHIGAN STATE UNIVERSITY · PI MIAS, GEORGE IOANNOU · 2014 to 2016
$745k
Integrative Dynamic Omics Profiling: A First Step Towards Personalized MedicineK99HG007065 · NHGRI · STANFORD UNIVERSITY · PI MIAS, GEORGE IOANNOU · 2013 to 2013
$90k
Intramural NIH HHS Z01 AI000887NHGRI NIH HHS K99 HG007065NHGRI NIH HHS K99HG007065NHGRI NIH HHS R00 HG007065NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG007919NIAID NIH HHS 1R01AI00887-01NIAID NIH HHS 4U54AI082973-04NIAID NIH HHS 5P01AI076210-04NIAID NIH HHS P01 AI076210NIAID NIH HHS R01 AI100887NIAID NIH HHS U54 AI082973
6 · The paper itself

Abstract

backgroundCombined immunodeficiency with multiple intestinal atresias (CID-MIA) is a rare hereditary disease characterized by intestinal obstructions and profound immune defects.

objectiveWe sought to determine the underlying genetic causes of CID-MIA by analyzing the exomic sequences of 5 patients and their healthy direct relatives from 5 unrelated families.

methodsWe performed whole-exome sequencing on 5 patients with CID-MIA and 10 healthy direct family members belonging to 5 unrelated families with CID-MIA. We also performed targeted Sanger sequencing for the candidate gene tetratricopeptide repeat domain 7A (TTC7A) on 3 additional patients with CID-MIA.

resultsThrough analysis and comparison of the exomic sequence of the subjects from these 5 families, we identified biallelic damaging mutations in the TTC7A gene, for a total of 7 distinct mutations. Targeted TTC7A gene sequencing in 3 additional unrelated patients with CID-MIA revealed biallelic deleterious mutations in 2 of them, as well as an aberrant splice product in the third patient. Staining of normal thymus showed that the TTC7A protein is expressed in thymic epithelial cells, as well as in thymocytes. Moreover, severe lymphoid depletion was observed in the thymus and peripheral lymphoid tissues from 2 patients with CID-MIA.

conclusionsWe identified deleterious mutations of the TTC7A gene in 8 unrelated patients with CID-MIA and demonstrated that the TTC7A protein is expressed in the thymus. Our results strongly suggest that TTC7A gene defects cause CID-MIA.

Indexed as

AnimalsChild, PreschoolExomeFemaleHumansImmunologic Deficiency SyndromesInfantInfant, NewbornIntestinal AtresiaIntestinesMaleMiceMutationOligonucleotide Array Sequence AnalysisProteinsRNA, MessengerProteinsRNA, MessengerTTC7A protein, humanTTC7 protein, mouseCID-MIACombined immunodeficiency with multiple intestinal atresiasGATKGenome Analysis ToolkitGraft-versus-host diseaseGvHDHCTHematopoietic cell transplantationIndelsInsertions and/or deletionsNMDNonsense-mediated decaySCIDSevere combined immunodeficiencySingle nucleotide variantSNVT-cell receptor excision circletetratricopeptide repeat domain 7ATetratricopeptide repeat domain 7AthymusTRECTTC7AWESwhole-exome sequencingWhole-exome sequencing

Identifiers

PMID23830146
PMCPMC3759618
OpenAlexW2120865353

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Read underepoch 390

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.