NDLI: GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data

Please wait, while we are loading the content...

GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data

Content Provider	Springer Nature : BioMed Central
Author	Yang, Xingyu Tipton, Christopher M. Woodruff, Matthew C. Zhou, Enlu Lee, F. Eun-Hyung Sanz, Inãki Qiu, Peng
Abstract	Background B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. Results We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure. Conclusions GLaMST outperforms state-of-art in reconstruction of the BCR lineage tree in both efficiency and accuracy. Integrating it into existing BCR sequencing analysis frameworks can significant improve lineage tree reconstruction aspect of the analysis.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-020-06936-w.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-020-06936-w
Journal	BMC Genomics
Issue Number	9
Volume Number	21
Language	English
Publisher	BioMed Central
Publisher Date	2020-09-09
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics B cell receptor gene Lineage tree
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data

Expansion of the HSFY gene family in pig lineages

VDJviz: a versatile browser for immunogenomics data

Inferring B cell specificity for vaccines using a Bayesian mixture model

Systems based analysis of human embryos and gene networks involved in cell lineage allocation

Inferring duplication episodes from unrooted gene trees

The effect of sequencing errors on metagenomic gene prediction

Erratum to: ‘Reference-free inference of tumor phylogenies from single-cell sequencing data’

Correction to: The effect of methanol fixation on single-cell RNA sequencing data

GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data

Similar Documents

GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data

Expansion of the HSFY gene family in pig lineages

VDJviz: a versatile browser for immunogenomics data

Inferring B cell specificity for vaccines using a Bayesian mixture model

Systems based analysis of human embryos and gene networks involved in cell lineage allocation

Inferring duplication episodes from unrooted gene trees

The effect of sequencing errors on metagenomic gene prediction

Erratum to: ‘Reference-free inference of tumor phylogenies from single-cell sequencing data’

Correction to: The effect of methanol fixation on single-cell RNA sequencing data

GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data