Tom Tang - Academia.edu (original) (raw)
Papers by Tom Tang
Background:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-5... more Background:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side comparison with Hiseq4000, on wellcharacterized human sample NA12878.Results:BGISEQ demonstrated similarly high reproducibility as Hiseq for variation detection. Also, the SNPs from BGISEQ data is highly consistent with Hiseq results (concordance 96.5%∼97%). Variation detection accuracy was subsequently evaluated with data from the genome in a bottle project as the benchmark. Both platforms showed similar sensitivity and precision in SNP detection. While in indel detection, BGISEQ showed slightly higher sensitivity and lower precision. The impact of sequence depth and read length on variation detection accuracy was further analyzed, and showed that variation detection sensitivi...
Nature, 2012
Recent advances in whole-genome sequencing have brought the vision of personal genomics and genom... more Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only 100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.
Nature communications, Jan 2, 2014
Mudskippers are amphibious fishes that have developed morphological and physiological adaptations... more Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in…
The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and... more The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human stem cell growth factor-like protein. These polynucleotides comprise nucleic acid sequences isolated from cDNA libraries from human testis cells (Hyseq clone identification numbers 2880984 and 2881695), from human fetal skin (Hyseq clone identification number 15375176), adult spleen (Hyseq clone identification number 14856094), and human endothelial cells (Hyseq clone identification numbers 13804756, 13687487, 13804756). Other aspects of the invention include vectors containing processes for producing novel human stem cell growth factor-like polypeptides, and antibodies specific for such polypeptides.
The invention relates to pharmaceutical compositions comprising gastrointestinal proliferative fa... more The invention relates to pharmaceutical compositions comprising gastrointestinal proliferative factor SCFA2, SCFA4 or SCFA4v polynucleotides and polypeptides. The invention further relates to the therapeutic use of SCFA2, SCFA4 or SCFA4v to prevent or treat conditions or disorders associated with the degeneration of the epithelial mucosa.
A gene encoding a polypeptide having an activity to support proliferation or survival of hematopo... more A gene encoding a polypeptide having an activity to support proliferation or survival of hematopoietic stem cells or hematopoietic progenitor cells is isolated by comparing expressed genes between cells which support proliferation or survival of hematopoietic stem cells or hematopoietic progenitor cells which do not support the proliferation or survival. Proliferation or survival of hematopoietic stem cells or hematopoietic progenitor cells is supported by using stromal cells in which the isolated gene is expressed or a gene product of the isolated gene.
The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and... more The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted stem cell growth factor-like polypeptides. Other aspects of the invention include vectors containing processes for producing novel human secreted stem cell growth factor-like polypeptides, and antibodies specific for such polypeptides
Lecture Notes Series, Institute for Mathematical Sciences, National University of Singapore, 2004
KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of ... more KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects. The KEGG project is undertaken in the Bioinformatics Center, Institute for Chemical Research, Kyoto University with supports from the Ministry of Education, Culture, Sports, Science and Technology and the Japan Society for the Promotion of Science.
Sertoli Cell Biology, 2005
Page 139. CHAPTER 9 Proteases and Protease Inhibitors MARTIN CHARRON AND WILLIAM W. WRIGHT Divisi... more Page 139. CHAPTER 9 Proteases and Protease Inhibitors MARTIN CHARRON AND WILLIAM W. WRIGHT Division of Reproductive Biology, Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health ...
2008 10th Electronics Packaging Technology Conference, 2008
This report experimentally demonstrated the fabrication and optimization of 45° micro-mirror form... more This report experimentally demonstrated the fabrication and optimization of 45° micro-mirror forming process in the polymer waveguide layer for optical interconections. The fluorinated acrylate waveguide is consisted of stacking of the lower cladding, core and upper cladding layer. The guide core (70 um �? 70 um) is fabricated by the soft molding method and the cladding layers are fabricated by
Currents in Computational Molecular …, 2000
Many organizations sequence cDNA clones from diverse tissue sources. Clustering and assembly of t... more Many organizations sequence cDNA clones from diverse tissue sources. Clustering and assembly of these sequences is a critical step for further genomic studies. Output from the clustering and assembly provides the expressed coding regions of genes with no introns, ...
Background:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-5... more Background:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side comparison with Hiseq4000, on wellcharacterized human sample NA12878.Results:BGISEQ demonstrated similarly high reproducibility as Hiseq for variation detection. Also, the SNPs from BGISEQ data is highly consistent with Hiseq results (concordance 96.5%∼97%). Variation detection accuracy was subsequently evaluated with data from the genome in a bottle project as the benchmark. Both platforms showed similar sensitivity and precision in SNP detection. While in indel detection, BGISEQ showed slightly higher sensitivity and lower precision. The impact of sequence depth and read length on variation detection accuracy was further analyzed, and showed that variation detection sensitivi...
Nature, 2012
Recent advances in whole-genome sequencing have brought the vision of personal genomics and genom... more Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only 100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.
Nature communications, Jan 2, 2014
Mudskippers are amphibious fishes that have developed morphological and physiological adaptations... more Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in…
The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and... more The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human stem cell growth factor-like protein. These polynucleotides comprise nucleic acid sequences isolated from cDNA libraries from human testis cells (Hyseq clone identification numbers 2880984 and 2881695), from human fetal skin (Hyseq clone identification number 15375176), adult spleen (Hyseq clone identification number 14856094), and human endothelial cells (Hyseq clone identification numbers 13804756, 13687487, 13804756). Other aspects of the invention include vectors containing processes for producing novel human stem cell growth factor-like polypeptides, and antibodies specific for such polypeptides.
The invention relates to pharmaceutical compositions comprising gastrointestinal proliferative fa... more The invention relates to pharmaceutical compositions comprising gastrointestinal proliferative factor SCFA2, SCFA4 or SCFA4v polynucleotides and polypeptides. The invention further relates to the therapeutic use of SCFA2, SCFA4 or SCFA4v to prevent or treat conditions or disorders associated with the degeneration of the epithelial mucosa.
A gene encoding a polypeptide having an activity to support proliferation or survival of hematopo... more A gene encoding a polypeptide having an activity to support proliferation or survival of hematopoietic stem cells or hematopoietic progenitor cells is isolated by comparing expressed genes between cells which support proliferation or survival of hematopoietic stem cells or hematopoietic progenitor cells which do not support the proliferation or survival. Proliferation or survival of hematopoietic stem cells or hematopoietic progenitor cells is supported by using stromal cells in which the isolated gene is expressed or a gene product of the isolated gene.
The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and... more The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted stem cell growth factor-like polypeptides. Other aspects of the invention include vectors containing processes for producing novel human secreted stem cell growth factor-like polypeptides, and antibodies specific for such polypeptides
Lecture Notes Series, Institute for Mathematical Sciences, National University of Singapore, 2004
KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of ... more KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects. The KEGG project is undertaken in the Bioinformatics Center, Institute for Chemical Research, Kyoto University with supports from the Ministry of Education, Culture, Sports, Science and Technology and the Japan Society for the Promotion of Science.
Sertoli Cell Biology, 2005
Page 139. CHAPTER 9 Proteases and Protease Inhibitors MARTIN CHARRON AND WILLIAM W. WRIGHT Divisi... more Page 139. CHAPTER 9 Proteases and Protease Inhibitors MARTIN CHARRON AND WILLIAM W. WRIGHT Division of Reproductive Biology, Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health ...
2008 10th Electronics Packaging Technology Conference, 2008
This report experimentally demonstrated the fabrication and optimization of 45° micro-mirror form... more This report experimentally demonstrated the fabrication and optimization of 45° micro-mirror forming process in the polymer waveguide layer for optical interconections. The fluorinated acrylate waveguide is consisted of stacking of the lower cladding, core and upper cladding layer. The guide core (70 um �? 70 um) is fabricated by the soft molding method and the cladding layers are fabricated by
Currents in Computational Molecular …, 2000
Many organizations sequence cDNA clones from diverse tissue sources. Clustering and assembly of t... more Many organizations sequence cDNA clones from diverse tissue sources. Clustering and assembly of these sequences is a critical step for further genomic studies. Output from the clustering and assembly provides the expressed coding regions of genes with no introns, ...