High-throughput sequencing and automated analysis of immunoglobulin genes: Life without a template

被引：0

作者：

Michaeli, Miri ^{[1
]}

Barak, Michal ^{[1
]}

Hazanov, Lena ^{[1
]}

Noga, Hila ^{[1
]}

Mehr, Ramit ^{[1
]}

机构：

[1] Bar Ilan Univ, Mina & Everard Goodman Fac Life Sci, IL-52900 Ramat Gan, Israel

来源：

PROCEEDINGS IWBBIO 2013: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING | 2013年

关键词：

DETECTING SELECTION; REPERTOIRE; ALIGNMENT; MEMORY;

D O I：

暂无

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. The introduction of high throughput sequencing has generated unprecedented amounts of repertoire and mutation data from immunoglobulin genes. However, common analysis programs are not appropriate for pre-processing and analyzing these data due to the lack of a template or reference gene. We present here the automated analysis pipeline we created for this purpose, which integrates various software packages of our own development and others', and demonstrate its performance.

引用

页码：19 / 26

页数：8

共 20 条

[1]

Ademokun A., 2011, AGING CELL

[2] IgTree©:: Creating immunoglobulin variable region gene lineage trees [J].

Barak, Michal ;

Zuckerman, Neta S. ;

Edelman, Hanna ;

Unger, Ron ;

Mehr, Ramit .

JOURNAL OF IMMUNOLOGICAL METHODS, 2008, 338 (1-2) :67-74

[3] Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements [J].

Boyd, Scott D. ;

Gaeta, Bruno A. ;

Jackson, Katherine J. ;

Fire, Andrew Z. ;

Marshall, Eleanor L. ;

Merker, Jason D. ;

Maniar, Jay M. ;

Zhang, Lyndon N. ;

Sahaf, Bita ;

Jones, Carol D. ;

Simen, Birgitte B. ;

Hanczaruk, Bozena ;

Nguyen, Khoa D. ;

Nadeau, Kari C. ;

Egholm, Michael ;

Miklos, David B. ;

Zehnder, James L. ;

Collins, Andrew M. .

JOURNAL OF IMMUNOLOGY, 2010, 184 (12) :6986-6992

[4] Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing [J].

Boyd, Scott D. ;

Marshall, Eleanor L. ;

Merker, Jason D. ;

Maniar, Jay M. ;

Zhang, Lyndon N. ;

Sahaf, Bita ;

Jones, Carol D. ;

Simen, Birgitte B. ;

Hanczaruk, Bozena ;

Nguyen, Khoa D. ;

Nadeau, Kari C. ;

Egholm, Michael ;

Miklos, David B. ;

Zehnder, James L. ;

Fire, Andrew Z. .

SCIENCE TRANSLATIONAL MEDICINE, 2009, 1 (12)

[5] Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing [J].

Campbell, Peter J. ;

Pleasance, Erin D. ;

Stephens, Philip J. ;

Dicks, Ed ;

Rance, Richard ;

Goodhead, Ian ;

Follows, George A. ;

Green, Anthony R. ;

Futreal, P. Andy ;

Stratton, Michael R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (35) :13081-13086

[6]

Dunn-Walters Deborah K, 2002, Dev Immunol, V9, P233, DOI 10.1080/10446670310001593541

[7] iHMMune-align:: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences [J].

Gaeta, Bruno A. ;

Malming, Harald R. ;

Jackson, Katherine J. L. ;

Bain, Michael E. ;

Wilson, Patrick ;

Collins, Andrew M. .

BIOINFORMATICS, 2007, 23 (13) :1580-1587

[8]

Giudicelli Veronique, 2011, Cold Spring Harb Protoc, V2011, P695, DOI 10.1101/pdb.prot5633

[9] Improved methods for detecting selection by mutation analysis of Ig V region sequences [J].

Hershberg, Uri ;

Uduman, Mohamed ;

Shlomchik, Mark J. ;

Kleinstein, Steven H. .

INTERNATIONAL IMMUNOLOGY, 2008, 20 (05) :683-694

[10]

Mehr R., 2012, IMMUNOL LETT

← 1 2 →