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120 results on '"Chaudhary, Ruchi"'

1. Safety and clinical activity of JNJ-78306358, a human leukocyte antigen-G (HLA-G) x CD3 bispecific antibody, for the treatment of advanced stage solid tumors

Author

Geva, Ravit, Vieito, Maria, Ramon, Jorge, Perets, Ruth, Pedregal, Manuel, Corral, Elena, Doger, Bernard, Calvo, Emiliano, Bardina, Jorge, Garralda, Elena, Brown, Regina J., Greger, James G., Wu, Shujian, Steinbach, Douglas, Yao, Tsun-Wen Sheena, Cao, Yu, Lauring, Josh, Chaudhary, Ruchi, Patel, Jaymala, Patel, Bharvin, and Moreno, Victor

Published
2024
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3. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity

Author

Wall, Jeffrey D, Sathirapongsasuti, J Fah, Gupta, Ravi, Rasheed, Asif, Venkatesan, Radha, Belsare, Saurabh, Menon, Ramesh, Phalke, Sameer, Mittal, Anuradha, Fang, John, Tanneeru, Deepak, Deshmukh, Manjari, Bassi, Akshi, Robinson, Jacqueline, Chaudhary, Ruchi, Murugan, Sakthivel, ul-Asar, Zameer, Saleem, Imran, Ishtiaq, Unzila, Fatima, Areej, Sheikh, Saqib Shafi, Hameed, Shahid, Ishaq, Mohammad, Rasheed, Syed Zahed, Memon, Fazal-ur-Rehman, Jalal, Anjum, Abbas, Shahid, Frossard, Philippe, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Bei, Qixin, Bhangale, Tushar, Tom, Jennifer, Gadde, Santosh Gopi Krishna, B V, Priya, Naik, Naveen Kumar, Wang, Minxian, Kwok, Pui-Yan, Khera, Amit V, Lakshmi, BR, Butterworth, Adam S, Chowdhury, Rajiv, Danesh, John, di Angelantonio, Emanuele, Naheed, Aliya, Goyal, Vinay, Kandadai, Rukmini M, Kumar, Hrishikesh, Borgohain, Rupam, Mukherjee, Adreesh, Wadia, Pettarusp M, Yadav, Ravi, Desai, Soaham, Kumar, Niraj, Biswas, Atanu, Pal, Pramod Kumar, Muthane, Uday B, Das, Shymal K, Ramprasad, Vedam L, Kukkle, Prashanth L, Seshagiri, Somasekar, Kathiresan, Sekar, Ghosh, Arkasubhra, Mohan, V, Saleheen, Danish, Stawiski, Eric W, and Peterson, Andrew S

Subjects
Genetics, Biotechnology, Clinical Research, Human Genome, Generic health relevance, Good Health and Well Being, Humans, Asian People, Bangladesh, Founder Effect, Homozygote, India, Pakistan, South Asian People
Abstract

The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.

Published
2023

4. South Asian Patient Population Genetics Reveal Strong Founder Effects and High Rates of Homozygosity – New Resources for Precision Medicine

Author

Wall, Jeffrey D, Sathirapongsasuti, J Fah, Gupta, Ravi, Barik, Anamitra, Rai, Rajesh Kumar, Rasheed, Asif, Radha, Venkatesan, Belsare, Saurabh, Menon, Ramesh, Phalke, Sameer, Mittal, Anuradha, Fang, John, Tanneeru, Deepak, Robinson, Jacqueline, Chaudhary, Ruchi, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Bei, Qixin, Bhangale, Tushar, Tom, Jennifer, Gadde, Santosh Gopi Krishna, Priya, BV, Naik, Naveen Kumar, Wang, Minxian, Kwok, Pui-Yan, Khera, Amit V, Lakshmi, BR, Butterworth, Adam, Danesh, John, Seshagiri, Sekar, Kathiresan, Sekar, Ghosh, Arkasubhra, Mohan, V, Chowdhury, Abhijit, Saleheen, Danish, Stawiski, Eric, and Peterson, Andrew S

Subjects
Genetics, Biotechnology, Human Genome, Clinical Research, Generic health relevance, Good Health and Well Being
Abstract

AbstractPopulation-scale genetic studies can identify drug targets and allow disease risk to be predicted with resulting benefit for management of individual health risks and system-wide allocation of health care delivery resources. Although population-scale projects are underway in many parts of the world, genetic variation between population groups means that additional projects are warranted. South Asia has a population whose genetics is the least characterized of any of the world’s major populations. Here we describe GenomeAsia studies that characterize population structure in South Asia and that create tools for economical and accurate genotyping at population-scale. Prior work on population structure characterized isolated population groups, the relevance of which to large-scale studies of disease genetics is unclear. For our studies we used whole genome sequence information from 4,807 individuals recruited in the health care delivery systems of Pakistan, India and Bangladesh to ensure relevance to population-scale studies of disease genetics. We combined this with WGS data from 927 individuals from isolated South Asian population groups, and developed a custom SNP array (called SARGAM) that is optimized for future human genetic studies in South Asia. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of homozygosity that approach 100 times that seen in outbred populations. We describe founder effects that increase the power to associate functional variants with disease processes and that make South Asia a uniquely powerful place for population-scale genetic studies.

Published
2020

5. Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis

Author

Chaudhary, Ruchi, Fernandez-Baca, David, and Burleigh, J. Gordon

Subjects
Computer Science - Data Structures and Algorithms
Abstract

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper provides a theoretical foundation for the use of TAGs in phylogenetics. We provide a formal definition of TAG that - unlike previous definition - does not depend on the order in which input trees are provided. In the consensus case, when all input trees have the same leaf labels, we describe algorithms for constructing majority-rule and strict consensus trees using the TAG. When the input trees do not have identical sets of leaf labels, we describe how to determine if the input trees are compatible and, if they are compatible, to construct a supertree that contains the input trees.

Published
2015

6. Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance

Author

Chaudhary, Ruchi, Burleigh, J. Gordon, and Fernández-Baca, David

Subjects
Computer Science - Data Structures and Algorithms, Quantitative Biology - Populations and Evolution
Abstract

We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can have the same label. Unlike most previous phylogenetic methods using gene trees, this method does not assume that gene tree incongruence is caused by a single, specific biological process, such as gene duplication and loss, deep coalescence, or lateral gene transfer. We prove that it is NP-hard to compute the RF distance between two mul-trees, but it is easy to calculate the generalized RF distance between a mul-tree and a singly-labeled tree. Motivated by this observation, we formulate the RF supertree problem for mul-trees (MulRF), which takes a collection of mul-trees and constructs a species tree that minimizes the total RF distance from the input mul-trees. We present a fast heuristic algorithm for the MulRF supertree problem. Simulation experiments demonstrate that the MulRF method produces more accurate species trees than gene tree parsimony methods when incongruence is caused by gene tree error, duplications and losses, and/or lateral gene transfer. Furthermore, the MulRF heuristic runs quickly on data sets containing hundreds of trees with up to a hundred taxa., Comment: 16 pages, 11 figures

Published
2012

7. iGTP: A software package for large-scale gene tree parsimony analysis

Author

Chaudhary, Ruchi, Bansal, Mukul S, Wehe, André, Fernández-Baca, David, and Eulenstein, Oliver

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Networking and Information Technology R&D (NITRD), Algorithms, Databases, Genetic, Evolution, Molecular, Gene Duplication, Genome, Genomics, Phylogeny, Software, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

BackgroundThe ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.ResultsWe introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results.ConclusionsiGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.

Published
2010

10. Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Author

Hinchliff, Cody E., Smith, Stephen A., Allman, James F., Burleigh, J. Gordon, Chaudhary, Ruchi, Coghill, Lyndon M., Crandall, Keith A., Deng, Jiabin, Drew, Bryan T., Gazis, Romina, Gude, Karl, Hibbett, David S., Katz, Laura A., Laughinghouse, H. Dail, McTavish, Emily Jane, Midford, Peter E., Owen, Christopher L., Ree, Richard H., Rees, Jonathan A., Soltis, Douglas E., Williams, Tiffani, and Cranston, Karen A.

Published
2015

12. Algorithms for Rapid Error Correction for the Gene Duplication Problem

Author

Chaudhary, Ruchi, Burleigh, J. Gordon, Eulenstein, Oliver, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Chen, Jianer, editor, Wang, Jianxin, editor, and Zelikovsky, Alexander, editor

Published
2011
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13. Fast Local Search for Unrooted Robinson-Foulds Supertrees

Author

Chaudhary, Ruchi, Burleigh, J. Gordon, Fernández-Baca, David, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Chen, Jianer, editor, Wang, Jianxin, editor, and Zelikovsky, Alexander, editor

Published
2011
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14. Genome‐Wide Polygenic Score Predicts Large Number of High Risk Individuals in Monogenic Undiagnosed Young Onset Parkinson's Disease Patients from India

Author

Kukkle, Prashanth Lingappa, primary, Geetha, Thenral S., additional, Chaudhary, Ruchi, additional, Sathirapongsasuti, Jarupon F., additional, Goyal, Vinay, additional, Kandadai, Rukmini Mridula, additional, Kumar, Hrishikesh, additional, Borgohain, Rupam, additional, Mukherjee, Adreesh, additional, Oliver, Merina, additional, Sunil, Meeta, additional, Mootor, Mohammed Faizal Eeman, additional, Kapil, Shruti, additional, Mandloi, Nitin, additional, Wadia, Pettarusp M., additional, Yadav, Ravi, additional, Desai, Soaham, additional, Kumar, Niraj, additional, Biswas, Atanu, additional, Pal, Pramod Kumar, additional, Muthane, Uday B., additional, Das, Shymal Kumar, additional, Sakthivel Murugan, Sakthivel M., additional, Peterson, Andrew S., additional, Stawiski, Eric W., additional, Seshagiri, Somasekar, additional, Gupta, Ravi, additional, Ramprasad, Vedam L., additional, and (PRAI), Parkinson Research Alliance of India, additional

Published
2022
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17. Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis

Author

Fenizia, Francesca, primary, Alborelli, Ilaria, additional, Costa, Jose Luis, additional, Vollbrecht, Claudia, additional, Bellosillo, Beatriz, additional, Dinjens, Winand, additional, Endris, Volker, additional, Heydt, Carina, additional, Leonards, Katharina, additional, Merkelback-Bruse, Sabine, additional, Pfarr, Nicole, additional, van Marion, Ronald, additional, Allen, Christopher, additional, Chaudhary, Ruchi, additional, Gottimukkala, Rajesh, additional, Hyland, Fiona, additional, Wong-Ho, Elaine, additional, Jermann, Philip, additional, Machado, Jose Carlos, additional, Hummel, Michael, additional, Stenzinger, Albrecht, additional, and Normanno, Nicola, additional

Published
2021
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18. Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis: Results from the Onconetwork Immuno-Oncology Consortium

Author

Fenizia, Francesca, Alborelli, Ilaria, Costa, Jose Luis, Vollbrecht, Claudia, Bellosillo, Beatriz, Dinjens, Winand, Endris, Volker, Heydt, Carina, Leonards, Katharina, Merkelback-Bruse, Sabine, Pfarr, Nicole, van Marion, Ronald, Allen, Christopher, Chaudhary, Ruchi, Gottimukkala, Rajesh, Hyland, Fiona, Wong-Ho, Elaine, Jermann, Philip, Machado, Jose Carlos, Hummel, Michael, Stenzinger, Albrecht, Normanno, Nicola, and Pathology

Subjects
DNA Mutational Analysis, High-Throughput Nucleotide Sequencing, Reproducibility of Results, DNA, DNA Mismatch Repair, Data Accuracy, Tumor Burden, SDG 3 - Good Health and Well-being, A549 Cells, Biomarkers, Tumor, MCF-7 Cells, Humans, Microsatellite Instability, Colorectal Neoplasms
Abstract

Tumor mutation burden (TMB) is evaluated as a biomarker of response to immunotherapy. We present the efforts of the Onconetwork Immuno-Oncology Consortium to validate a commercial targeted sequencing test for TMB calculation. A three-phase study was designed to validate the Oncomine Tumor Mutational Load (OTML) assay at nine European laboratories. Phase 1 evaluated reproducibility and accuracy on seven control samples. In phase 2, six formalin-fixed, paraffin-embedded samples tested with FoundationOne were reanalyzed with the OTML panel to evaluate concordance and reproducibility. Phase 3 involved analysis of 90 colorectal cancer samples with known microsatellite instability (MSI) status to evaluate TMB and MSI association. High reproducibility of TMB was demonstrated among the sites in the first and second phases. Strong correlation was also detected between mean and expected TMB in phase 1 (r2 = 0.998) and phase 2 (r2 = 0.96). Detection of actionable mutations was also confirmed. In colorectal cancer samples, the expected pattern of MSI-high/high-TMB and microsatellite stability/low-TMB was present, and gene signatures produced by the panel suggested the presence of a POLE mutation in two samples. The OTML panel demonstrated robustness and reproducibility for TMB evaluation. Results also suggest the possibility of using the panel for mutational signatures and variant detection. Collaborative efforts between academia and companies are crucial to accelerate the translation of new biomarkers into clinical research.

Published
2020

19. Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence

Author

Chaudhary Ruchi, Burleigh J Gordon, and Eulenstein Oliver

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. Gene tree parsimony approaches seek the evolutionary scenario that implies the fewest gene duplications, duplications and losses, or deep coalescence (incomplete lineage sorting) events needed to reconcile a gene tree and a species tree. While a gene tree parsimony approach can be informative about genome evolution and phylogenetics, error in gene trees can profoundly bias the results. Results We introduce efficient algorithms that rapidly search local Subtree Prune and Regraft (SPR) or Tree Bisection and Reconnection (TBR) neighborhoods of a given gene tree to identify a topology that implies the fewest duplications, duplication and losses, or deep coalescence events. These algorithms improve on the current solutions by a factor of n for searching SPR neighborhoods and n2 for searching TBR neighborhoods, where n is the number of taxa in the given gene tree. They provide a fast error correction protocol for ameliorating the effects of gene tree error by allowing small rearrangements in the topology to improve the reconciliation cost. We also demonstrate a simple protocol to use the gene rearrangement algorithm to improve gene tree parsimony phylogenetic analyses. Conclusions The new gene tree rearrangement algorithms provide a fast method to address gene tree error. They do not make assumptions about the underlying processes of genome evolution, and they are amenable to analyses of large-scale genomic data sets. These algorithms are also easily incorporated into gene tree parsimony phylogenetic analyses, potentially producing more credible estimates of reconciliation cost.

Published
2012
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24. South Asian Patient Population Genetics Reveal Strong Founder Effects and High Rates of Homozygosity – New Resources for Precision Medicine

Author

Wall, Jeffrey D., primary, Sathirapongsasuti, J. Fah, additional, Gupta, Ravi, additional, Barik, Anamitra, additional, Rai, Rajesh Kumar, additional, Rasheed, Asif, additional, Radha, Venkatesan, additional, Belsare, Saurabh, additional, Menon, Ramesh, additional, Phalke, Sameer, additional, Mittal, Anuradha, additional, Fang, John, additional, Tanneeru, Deepak, additional, Robinson, Jacqueline, additional, Chaudhary, Ruchi, additional, Fuchsberger, Christian, additional, Forer, Lukas, additional, Schoenherr, Sebastian, additional, Bei, Qixin, additional, Bhangale, Tushar, additional, Tom, Jennifer, additional, Krishna Gadde, Santosh Gopi, additional, Priya, B. V., additional, Naik, Naveen Kumar, additional, Wang, Minxian, additional, Kwok, Pui-Yan, additional, Khera, Amit V., additional, Lakshmi, B. R., additional, Butterworth, Adam, additional, Danesh, John, additional, Seshagiri, Sekar, additional, Kathiresan, Sekar, additional, Ghosh, Arkasubhra, additional, Mohan, V., additional, Chowdhury, Abhijit, additional, Saleheen, Danish, additional, Stawiski, Eric, additional, and Peterson, Andrew S., additional

Published
2020
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26. Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the Friends of Cancer Research TMB Harmonization Project

Author

Merino, Diana M, primary, McShane, Lisa M, additional, Fabrizio, David, additional, Funari, Vincent, additional, Chen, Shu-Jen, additional, White, James R, additional, Wenz, Paul, additional, Baden, Jonathan, additional, Barrett, J Carl, additional, Chaudhary, Ruchi, additional, Chen, Li, additional, Chen, Wangjuh (Sting), additional, Cheng, Jen-Hao, additional, Cyanam, Dinesh, additional, Dickey, Jennifer S, additional, Gupta, Vikas, additional, Hellmann, Matthew, additional, Helman, Elena, additional, Li, Yali, additional, Maas, Joerg, additional, Papin, Arnaud, additional, Patidar, Rajesh, additional, Quinn, Katie J, additional, Rizvi, Naiyer, additional, Tae, Hongseok, additional, Ward, Christine, additional, Xie, Mingchao, additional, Zehir, Ahmet, additional, Zhao, Chen, additional, Dietel, Manfred, additional, Stenzinger, Albrecht, additional, Stewart, Mark, additional, and Allen, Jeff, additional

Published
2020
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27. South Asian Patient Population Genetics Reveal Strong Founder Effects and High Rates of Homozygosity – New Resources for Precision Medicine

Author

Wall, Jeff D., primary, Sathirapongsasuti, J. Fah, additional, Gupta, Ravi, additional, Barik, Anamitra, additional, Rai, Rajesh Kumar, additional, Rasheed, Asif, additional, Radha, Venkatesan, additional, Belsare, Saurabh, additional, Menon, Ramesh, additional, Phalke, Sameer, additional, Mittal, Anuradha, additional, Fang, John, additional, Tanneeru, Deepak, additional, Deshmukh, Manjari, additional, Bassi, Akshi, additional, Robinson, Jacqueline, additional, Chaudhary, Ruchi, additional, Asar, Zameer-ul, additional, Saleem, Imran, additional, Ishtiaq, Unzila, additional, Fatima, Areej, additional, Sheikh, Saqib Shafi, additional, Hameed, Shahid, additional, Ishaq, Mohammad, additional, Rasheed, Syed Zahed, additional, Memon, Fazal-ur-Rehman, additional, Jalal, Anjum, additional, Abbas, Shahid, additional, Frossard, Philippe, additional, Fuchsberger, Christian, additional, Forer, Lukas, additional, Schoenherr, Sebastian, additional, Bei, Qixin, additional, Bhangale, Tushar, additional, Tom, Jennifer, additional, Gadde, Santosh Gopi Krishna, additional, V., Priya B., additional, Naik, Naveen Kumar, additional, Wang, Minxian, additional, Kwok, Pui-Yan, additional, Khera, Amit V., additional, Lakshmi, B. R., additional, Butterworth, Adam S., additional, Chowdhury, Rajiv, additional, Danesh, John, additional, di Angelantonio, Emanuele, additional, Naheed, Aliya, additional, Seshagiri, Sekar, additional, Kathiresan, Sekar, additional, Ghosh, Arkasubhra, additional, Mohan, V., additional, Chowdhury, Abhijit, additional, Saleheen, Danish, additional, Stawiski, Eric, additional, and Peterson, Andrew S., additional

Published
2020
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31. iGTP: A software package for large-scale gene tree parsimony analysis

Author

Fernández-Baca David, Wehe André, Bansal Mukul S, Chaudhary Ruchi, and Eulenstein Oliver

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle. Results We introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results. Conclusions iGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.

Published
2010
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39. Comprehensive detection of ctDNA variants at 0.1% allelic frequency using a broad targeted NGS panel for liquid biopsy research.

Author

Chien, Richard, primary, Brinza, Dumitru, additional, Gu, Jian, additional, Dhingra, Dalia, additional, Banjara, Kunal, additional, Li, Yanchun, additional, Bagai, Varun, additional, Schageman, Jeoffrey, additional, Ballesteros-Villagrana, Efren, additional, Chaudhary, Ruchi, additional, Hanif, Khalid, additional, Au-Young, Janice, additional, Hyland, Fiona, additional, and Bramlett, Kelli, additional

Published
2017
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42. Outcomes of Myeloablative Haplo-Identical Hematopoietic Stem Cell Transplant in Pediatric Patients with TCR α/β and CD 19 Depletion

Author

Bhat, Sunil, primary, Ngangbam, Sonamani, additional, Iqbal, Waseem, additional, Badiger, Shobha, additional, Nataraj, K.S., additional, Chakraborty, Sohini, additional, Damodar, Sharat, additional, Chaudhary, Ruchi, additional, Prathip, B.R., additional, Hailu, Tadele, additional, and Chezhian, Nedun, additional

Published
2017
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