Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes

被引:0
|
作者
Shamil Sunyaev
Jens Hanke
Atakan Aydin
Ute Wirkner
Inga Zastrow
Jens Reich
Peer Bork
机构
[1] EMBL,
[2] Meyerhofstrasse 1,undefined
[3] D-69012 Heidelberg,undefined
[4] Max Delbrück Center for Molecular Medicine,undefined
[5] Berlin-Buch,undefined
[6] Franz-Volhard Clinic,undefined
[7] Max Delbrück Center for Molecular Medicine,undefined
[8] Virchow Klinikum,undefined
[9] Berlin-Buch,undefined
来源
Journal of Molecular Medicine | 1999年 / 77卷
关键词
Single nucleotide polymorphism Disease-associated genes Expressed sequence tag database;
D O I
暂无
中图分类号
学科分类号
摘要
Analysis of human genetic variation can shed light on the problem of the genetic basis of complex disorders. Nonsynonymous single nucleotide polymorphisms (SNPs), which affect the amino acid sequence of proteins, are believed to be the most frequent type of variation associated with the respective disease phenotype. Complete enumeration of nonsynonymous SNPs in the candidate genes will enable further association studies on panels of affected and unaffected individuals. Experimental detection of SNPs requires implementation of expensive technologies and is still far from being routine. Alternatively, SNPs can be identified by computational analysis of a publicly available expressed sequence tag (EST) database following experimental verification. We performed in silico analysis of amino acid variation for 471 of proteins with a documented history of experimental variation studies and with confirmed association with human diseases. This allowed us to evaluate the level of completeness of the current knowledge of nonsynonymous SNPs in well studied, medically relevant genes and to estimate the proportion of new variants which can be added with the help of computer-aided mining in EST databases. Our results suggest that approx. 50% of frequent nonsynonymous variants are already stored in public databases. Computational methods based on the scan of an EST database can add significantly to the current knowledge, but they are greatly limited by the size of EST databases and the nonuniform coverage of genes by ESTs. Nevertheless, a considerable number of new candidate nonsynonymous SNPs in genes of medical interest were found by EST screening procedure.
引用
收藏
页码:754 / 760
页数:6
相关论文
共 50 条
  • [21] Candidate genes and single nucleotide polymorphisms (SNPs) in the study of human disease
    Chanock, S
    DISEASE MARKERS, 2001, 17 (02) : 89 - 98
  • [22] In Silico Prediction of the Effects of Nonsynonymous Single Nucleotide Polymorphisms in the Human Catechol-O-Methyltransferase (COMT) Gene
    Akin Yilmaz
    İhsan Çetin
    Cell Biochemistry and Biophysics, 2020, 78 : 227 - 239
  • [23] EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome
    Zeng, Shuai
    Yang, Jing
    Chung, Brian Hon-Yin
    Lau, Yu Lung
    Yang, Wanling
    BMC GENOMICS, 2014, 15
  • [24] EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome
    Shuai Zeng
    Jing Yang
    Brian Hon-Yin Chung
    Yu Lung Lau
    Wanling Yang
    BMC Genomics, 15
  • [25] Association Study of Nonsynonymous Single Nucleotide Polymorphisms in Schizophrenia
    Carrera, Noa
    Arrojo, Manuel
    Sanjuan, Julio
    Ramos-Rios, Ramon
    Paz, Eduardo
    Suarez-Rama, Jose J.
    Paramo, Mario
    Agra, Santiago
    Brenlla, Julio
    Martinez, Silvia
    Rivero, Olga
    Collier, David A.
    Palotie, Aarno
    Cichon, Sven
    Noethen, Markus M.
    Rietschel, Marcella
    Rujescu, Dan
    Stefansson, Hreinn
    Steinberg, Stacy
    Sigurdsson, Engilbert
    St Clair, David
    Tosato, Sarah
    Werge, Thomas
    Stefansson, Kari
    Carlos Gonzalez, Jose
    Valero, Joaquin
    Gutierez-Zotes, Alfonso
    Labad, Antonio
    Martorell, Lourdes
    Vilella, Elisabet
    Carracedo, Angel
    Costas, Javier
    BIOLOGICAL PSYCHIATRY, 2012, 71 (02) : 169 - 177
  • [26] Prediction of Deleterious Nonsynonymous Single-Nucleotide Polymorphism for Human Diseases
    Wu, Jiaxin
    Jiang, Rui
    SCIENTIFIC WORLD JOURNAL, 2013,
  • [27] Prediction and assessment of deleterious and disease causing nonsynonymous single nucleotide polymorphisms (nsSNPs) in human FOXP4 gene: An in-silico study
    Kamal, Md. Mostafa
    Teeya, Shamiha Tabassum
    Rahman, Md. Mahfuzur
    Talukder, Md. Enamul Kabir
    Sarmin, Sonia
    Wani, Tanveer A.
    Hasan, Md. Mahmudul
    HELIYON, 2024, 10 (12)
  • [28] Structural and Functional Analysis of Deleterious Nonsynonymous Single Nucleotide Polymorphisms in PAH Associated with Phenylketonuria
    Doss, C. George Priya
    Sethumadhavan, Rao
    ADVANCED SCIENCE LETTERS, 2009, 2 (03) : 364 - 371
  • [29] Non-neutral nonsynonymous single nucleotide polymorphisms in human ABC transporters: the first comparison of six prediction methods
    Hao, Da Cheng
    Feng, Yao
    Xiao, Rongrong
    Xiao, Pei Gen
    PHARMACOLOGICAL REPORTS, 2011, 63 (04) : 924 - 934
  • [30] Non-neutral nonsynonymous single nucleotide polymorphisms in human ABC transporters: the first comparison of six prediction methods
    Da Cheng Hao
    Yao Feng
    Rongrong Xiao
    Pei Gen Xiao
    Pharmacological Reports, 2011, 63 : 924 - 934