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Patient complexity and genotype-phenotype correlations in biliary atresia: a cross-sectional analysis.

Abstract Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering the BA phenotypic variance is a priority in clinics and can be achieved by the integrative analysis of genotype and phenotype. We aim to explore the BA phenotypic features and to delineate the source of its variance.
PMID
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Authors

Mayor MeshTerms
Keywords

Copy number variant

Genotype-phenotype correlation

Network

Rare complex disease

Journal Title bmc medical genomics
Publication Year Start




PMID- 28416017
OWN - NLM
STAT- In-Process
DA  - 20170418
LR  - 20170421
IS  - 1755-8794 (Electronic)
IS  - 1755-8794 (Linking)
VI  - 10
IP  - 1
DP  - 2017 Apr 17
TI  - Patient complexity and genotype-phenotype correlations in biliary atresia: a
      cross-sectional analysis.
PG  - 22
LID - 10.1186/s12920-017-0259-0 [doi]
AB  - BACKGROUND: Biliary Atresia (BA) is rare and genetically complex, and the
      pathogenesis is elusive. The disease course is variable and can represent
      heterogeneity, which hinders effective disease management. Deciphering the BA
      phenotypic variance is a priority in clinics and can be achieved by the
      integrative analysis of genotype and phenotype. We aim to explore the BA
      phenotypic features and to delineate the source of its variance. METHODS: The
      study is a cross-sectional observational study collating with case/control
      association analysis. One-hundred-and-eighty-one type III non-syndromic BA
      patients and 431 controls were included for case-control association tests,
      including 89 patients (47.19% males, born June 15th, 1981 to September 17th,
      2007) have detailed clinical records with follow-up of the disease course (median
      ~17.2 years). BA-association genes from the genome-wide gene-based association
      test on common genetic variants (CV) and rare copy-number-variants (CNVs) from
      the genome-wide survey, the later comprise only CNVs > 100 kb and found in the BA
      patients but not in the local population (N = 1,381) or the database (N =
      11,943). Hereby comorbidity is defined as a chronic disease that affects the BA
      patients but has no known relationship with BA or with the BA treatment. We
      examined genotype-phenotype correlations of CNVs, connectivity of these novel
      variants with BA-associated CVs, and their role in the BA candidate gene network.
      RESULTS: Of the 89 patients, 41.57% have comorbidities, including
      autoimmune-allergic disorders (22.47%). They carried 29 BA-private CNVs,
      including 3 CNVs underpinning the carriers' immunity comorbidity and one JAG1
      micro-deletion. The BA-CNV-intersected genes (N = 102) and the CV-tagged genes (N
      = 103) were both enriched with immune-inflammatory pathway genes (FDR q < 0.20), 
      and the two gene sets were interconnected (permutation p = 0.039). The molecular 
      network representing CVs and rare-CNV association genes fit into a core/periphery
      structure, the immune genes and their related modules are found at the coherence 
      core of all connections, suggesting its dominant role in the BA pathogenesis
      pathway. CONCLUSIONS: The study highlights a patient-complexity phenomenon as a
      novel BA phenotypic feature, which is underpinned by rare-CNVs that biologically 
      converge with CVs into the immune-inflammatory pathway and drives the BA
      occurrence and the likely BA association with immune diseases in clinics.
FAU - Cheng, Guo
AU  - Cheng G
AD  - Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary
      Research, 5 Sassoon Road, Pokfulam, Hong Kong.
FAU - Chung, Patrick Ho-Yu
AU  - Chung PH
AD  - Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary
      Research, 5 Sassoon Road, Pokfulam, Hong Kong.
FAU - Chan, Edwin Kin-Wai
AU  - Chan EK
AD  - Department of Surgery, the Chinese University of Hong Kong, Hong Kong, SAR,
      China.
FAU - So, Man-Ting
AU  - So MT
AD  - Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary
      Research, 5 Sassoon Road, Pokfulam, Hong Kong.
FAU - Sham, Pak-Chung
AU  - Sham PC
AD  - Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.
AD  - Center for Genomic Sciences, Hong Kong, SAR, China.
AD  - Centre for Reproduction, Development, Growth of the Li Ka Shing Faculty of
      Medicine, Hong Kong, SAR, China.
AD  - State Key Laboratory of Brain and Cognitive Sciences, The University of Hong
      Kong, Hong Kong, SAR, China.
FAU - Cherny, Stacey S
AU  - Cherny SS
AD  - Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.
AD  - Center for Genomic Sciences, Hong Kong, SAR, China.
AD  - State Key Laboratory of Brain and Cognitive Sciences, The University of Hong
      Kong, Hong Kong, SAR, China.
FAU - Tam, Paul Kwong-Hang
AU  - Tam PK
AD  - Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary
      Research, 5 Sassoon Road, Pokfulam, Hong Kong.
AD  - Centre for Reproduction, Development, Growth of the Li Ka Shing Faculty of
      Medicine, Hong Kong, SAR, China.
FAU - Garcia-Barcelo, Maria-Merce
AU  - Garcia-Barcelo MM
AD  - Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary
      Research, 5 Sassoon Road, Pokfulam, Hong Kong. [email protected]
AD  - Center for Genomic Sciences, Hong Kong, SAR, China. [email protected]
AD  - Centre for Reproduction, Development, Growth of the Li Ka Shing Faculty of
      Medicine, Hong Kong, SAR, China. [email protected]
LA  - eng
PT  - Journal Article
DEP - 20170417
PL  - England
TA  - BMC Med Genomics
JT  - BMC medical genomics
JID - 101319628
PMC - PMC5392958
OTO - NOTNLM
OT  - Copy number variant
OT  - Genotype-phenotype correlation
OT  - Network
OT  - Rare complex disease
EDAT- 2017/04/19 06:00
MHDA- 2017/04/19 06:00
CRDT- 2017/04/19 06:00
PHST- 2016/08/17 [received]
PHST- 2017/04/05 [accepted]
AID - 10.1186/s12920-017-0259-0 [doi]
AID - 10.1186/s12920-017-0259-0 [pii]
PST - epublish
SO  - BMC Med Genomics. 2017 Apr 17;10(1):22. doi: 10.1186/s12920-017-0259-0.

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