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Start Over Author "Fungtammasan A" Journal nature biotechnology
5 results on '"Fungtammasan A"'

1. Curated variation benchmarks for challenging medically relevant autosomal genes

Author

Wagner, Justin, primary, Olson, Nathan D., additional, Harris, Lindsay, additional, McDaniel, Jennifer, additional, Cheng, Haoyu, additional, Fungtammasan, Arkarachai, additional, Hwang, Yih-Chii, additional, Gupta, Richa, additional, Wenger, Aaron M., additional, Rowell, William J., additional, Khan, Ziad M., additional, Farek, Jesse, additional, Zhu, Yiming, additional, Pisupati, Aishwarya, additional, Mahmoud, Medhat, additional, Xiao, Chunlin, additional, Yoo, Byunggil, additional, Sahraeian, Sayed Mohammad Ebrahim, additional, Miller, Danny E., additional, Jáspez, David, additional, Lorenzo-Salazar, José M., additional, Muñoz-Barrera, Adrián, additional, Rubio-Rodríguez, Luis A., additional, Flores, Carlos, additional, Narzisi, Giuseppe, additional, Evani, Uday Shanker, additional, Clarke, Wayne E., additional, Lee, Joyce, additional, Mason, Christopher E., additional, Lincoln, Stephen E., additional, Miga, Karen H., additional, Ebbert, Mark T. W., additional, Shumate, Alaina, additional, Li, Heng, additional, Chin, Chen-Shan, additional, Zook, Justin M., additional, and Sedlazeck, Fritz J., additional

Published
2022
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2. Curated variation benchmarks for challenging medically relevant autosomal genes

Author

Justin Wagner, Nathan D. Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M. Wenger, William J. Rowell, Ziad M. Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E. Miller, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz-Barrera, Luis A. Rubio-Rodríguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E. Clarke, Joyce Lee, Christopher E. Mason, Stephen E. Lincoln, Karen H. Miga, Mark T. W. Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M. Zook, and Fritz J. Sedlazeck

Subjects
Haplotypes, Genome, Human, Biomedical Engineering, Molecular Medicine, Humans, Bioengineering, Sequence Analysis, DNA, Applied Microbiology and Biotechnology, Biotechnology
Abstract

The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome.

Published
2021

3. Chromosome-scale, haplotype-resolved assembly of human genomes

Author

Garg, Shilpa, primary, Fungtammasan, Arkarachai, additional, Carroll, Andrew, additional, Chou, Mike, additional, Schmitt, Anthony, additional, Zhou, Xiang, additional, Mac, Stephen, additional, Peluso, Paul, additional, Hatas, Emily, additional, Ghurye, Jay, additional, Maguire, Jared, additional, Mahmoud, Medhat, additional, Cheng, Haoyu, additional, Heller, David, additional, Zook, Justin M., additional, Moemke, Tobias, additional, Marschall, Tobias, additional, Sedlazeck, Fritz J., additional, Aach, John, additional, Chin, Chen-Shan, additional, Church, George M., additional, and Li, Heng, additional

Published
2020
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4. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Author

Wenger, Aaron M., primary, Peluso, Paul, additional, Rowell, William J., additional, Chang, Pi-Chuan, additional, Hall, Richard J., additional, Concepcion, Gregory T., additional, Ebler, Jana, additional, Fungtammasan, Arkarachai, additional, Kolesnikov, Alexey, additional, Olson, Nathan D., additional, Töpfer, Armin, additional, Alonge, Michael, additional, Mahmoud, Medhat, additional, Qian, Yufeng, additional, Chin, Chen-Shan, additional, Phillippy, Adam M., additional, Schatz, Michael C., additional, Myers, Gene, additional, DePristo, Mark A., additional, Ruan, Jue, additional, Marschall, Tobias, additional, Sedlazeck, Fritz J., additional, Zook, Justin M., additional, Li, Heng, additional, Koren, Sergey, additional, Carroll, Andrew, additional, Rank, David R., additional, and Hunkapiller, Michael W., additional

Published
2019
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5. Chromosome-scale, haplotype-resolved assembly of human genomes.

Author

Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, and Chin, Chen-Shan

Abstract

Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98–99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity. Assembly of phased human genomes is achieved by combining long reads and long-range conformational data. [ABSTRACT FROM AUTHOR]

Published
2021
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