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  1. Article ; Online: Bioinformatics in Clinical Genomic Sequencing.

    Lebo, Matthew S / Hao, Limin / Lin, Chiao-Feng / Singh, Arti

    Clinics in laboratory medicine

    2020  Volume 40, Issue 2, Page(s) 163–187

    MeSH term(s) Computational Biology ; Humans ; Sequence Analysis, DNA ; Whole Genome Sequencing
    Language English
    Publishing date 2020-07-12
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 604580-7
    ISSN 1557-9832 ; 0272-2712
    ISSN (online) 1557-9832
    ISSN 0272-2712
    DOI 10.1016/j.cll.2020.02.003
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  2. Article ; Online: Automated Pharmacogenomic Reports for Clinical Genome Sequencing.

    Klanderman, Barbara J / Koch, Christopher / Machini, Kalotina / Parpattedar, Shruti S / Bandyadka, Shruthi / Lin, Chiao-Feng / Hynes, Elizabeth / Lebo, Matthew S / Amr, Sami S

    The Journal of molecular diagnostics : JMD

    2022  Volume 24, Issue 3, Page(s) 205–218

    Abstract: Clinical laboratories offering genome sequencing have the opportunity to return pharmacogenomic findings to patients, providing the added benefit of preemptive testing that could help inform medication selection or dosing throughout the lifespan. ... ...

    Abstract Clinical laboratories offering genome sequencing have the opportunity to return pharmacogenomic findings to patients, providing the added benefit of preemptive testing that could help inform medication selection or dosing throughout the lifespan. Implementation of pharmacogenomic reporting must address several challenges, including inherent limitations in short-read genome sequencing methods, gene and variant selection, standardization of genotype and phenotype nomenclature, and choice of guidelines and drugs to report. An automated pipeline, lmPGX, was developed as an end-to-end solution that produces two versions of a pharmacogenomic report, presenting either Clinical Pharmacogenetics Implementation Consortium or US Food and Drug Administration guidelines for 12 genes. The pipeline was validated for performance using reference samples and pharmacogenetic data from the Genetic Testing Reference Materials Coordination Program. To determine performance and limitations, lmPGX was compared with three additional publicly available pharmacogenomic pipelines. The lmPGX pipeline offers clinical laboratories an opportunity for seamless integration of pharmacogenomic results with genome reporting.
    MeSH term(s) Genetic Testing ; Genotype ; Humans ; Pharmacogenetics/methods ; Pharmacogenomic Testing/methods ; Phenotype
    Language English
    Publishing date 2022-01-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2000060-1
    ISSN 1943-7811 ; 1525-1578
    ISSN (online) 1943-7811
    ISSN 1525-1578
    DOI 10.1016/j.jmoldx.2021.12.001
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  3. Article ; Online: Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests.

    Lin, Chiao-Feng / Naj, Adam C / Wang, Li-San

    Current protocols in human genetics

    2013  Volume 79, Page(s) Unit 1.27.

    Abstract: High-density SNP genotyping technology provides a low-cost, effective tool for conducting Genome Wide Association (GWA) studies. The wide adoption of GWA studies has indeed led to discoveries of disease- or trait-associated SNPs, some of which were ... ...

    Abstract High-density SNP genotyping technology provides a low-cost, effective tool for conducting Genome Wide Association (GWA) studies. The wide adoption of GWA studies has indeed led to discoveries of disease- or trait-associated SNPs, some of which were subsequently shown to be causal. However, the nearly universal shortcoming of many GWA studies--missing heritability--has prompted great interest in searching for other types of genetic variation, such as copy number variation (CNV). Certain CNVs have been reported to alter disease susceptibility. Algorithms and tools have been developed to identify CNVs using SNP array hybridization intensity data. Such an approach provides an additional source of data with almost no extra cost. In this unit, we demonstrate the steps for calling CNVs from Illumina SNP array data using PennCNV and performing association analysis using R and PLINK.
    MeSH term(s) Algorithms ; DNA Copy Number Variations ; Gene Frequency ; Genome-Wide Association Study/methods ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2013-10-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2179054-1
    ISSN 1934-8258 ; 1934-8266
    ISSN (online) 1934-8258
    ISSN 1934-8266
    DOI 10.1002/0471142905.hg0127s79
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  4. Article ; Online: Evolutionary dynamics of U12-type spliceosomal introns

    Mount Stephen M / Lin Chiao-Feng / Jarmołowski Artur / Makałowski Wojciech

    BMC Evolutionary Biology, Vol 10, Iss 1, p

    2010  Volume 47

    Abstract: Abstract Background Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor ( ...

    Abstract Abstract Background Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly. Results We have investigated the evolution of U12-type introns among eighteen metazoan genomes by analyzing orthologous U12-type intron clusters. Examination of gain, loss, and type switching shows that intron type is remarkably conserved among vertebrates. Among 180 intron clusters, only eight show intron loss in any vertebrate species and only five show conversion between the U12 and the U2-type. Although there are only nineteen U12-type introns in Drosophila melanogaster , we found one case of U2 to U12-type conversion, apparently mediated by the activation of cryptic U12 splice sites early in the dipteran lineage. Overall, loss of U12-type introns is more common than conversion to U2-type and the U12 to U2 conversion occurs more frequently among introns of the GT-AG subtype than among introns of the AT-AC subtype. We also found support for natural U12-type introns with non-canonical terminal dinucleotides (CT-AC, GG-AG, and GA-AG) that have not been previously reported. Conclusions Although complete loss of the U12-type spliceosome has occurred repeatedly, U12 introns are extremely stable in some taxa, including eutheria. Loss of U12 introns or the genes containing them is more common than conversion to the U2-type. The degeneracy of U12-type terminal dinucleotides among natural U12-type introns is higher than previously thought.
    Keywords Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Evolution ; QH359-425
    Subject code 590
    Language English
    Publishing date 2010-02-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Birth and death of gene overlaps in vertebrates

    Makałowska Izabela / Lin Chiao-Feng / Hernandez Krisitina

    BMC Evolutionary Biology, Vol 7, Iss 1, p

    2007  Volume 193

    Abstract: Abstract Background Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although ... ...

    Abstract Abstract Background Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin. Results Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap. Conclusion Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.
    Keywords Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Evolution ; QH359-425
    Subject code 612
    Language English
    Publishing date 2007-10-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
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  6. Article ; Online: A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing.

    Lincoln, Stephen E / Truty, Rebecca / Lin, Chiao-Feng / Zook, Justin M / Paul, Joshua / Ramey, Vincent H / Salit, Marc / Rehm, Heidi L / Nussbaum, Robert L / Lebo, Matthew S

    The Journal of molecular diagnostics : JMD

    2019  Volume 21, Issue 2, Page(s) 318–329

    Abstract: Orthogonal confirmation of next-generation sequencing (NGS)-detected germline variants is standard practice, although published studies have suggested that confirmation of the highest-quality calls may not always be necessary. The key question is how ... ...

    Abstract Orthogonal confirmation of next-generation sequencing (NGS)-detected germline variants is standard practice, although published studies have suggested that confirmation of the highest-quality calls may not always be necessary. The key question is how laboratories can establish criteria that consistently identify those NGS calls that require confirmation. Most prior studies addressing this question have had limitations: they have been generally of small scale, omitted statistical justification, and explored limited aspects of underlying data. The rigorous definition of criteria that separate high-accuracy NGS calls from those that may or may not be true remains a crucial issue. We analyzed five reference samples and over 80,000 patient specimens from two laboratories. Quality metrics were examined for approximately 200,000 NGS calls with orthogonal data, including 1662 false positives. A classification algorithm used these data to identify a battery of criteria that flag 100% of false positives as requiring confirmation (CI lower bound, 98.5% to 99.8%, depending on variant type) while minimizing the number of flagged true positives. These criteria identify false positives that the previously published criteria miss. Sampling analysis showed that smaller data sets resulted in less effective criteria. Our methodology for determining test- and laboratory-specific criteria can be generalized into a practical approach that can be used by laboratories to reduce the cost and time burdens of confirmation without affecting clinical accuracy.
    MeSH term(s) Algorithms ; Genetic Testing/methods ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA
    Language English
    Publishing date 2019-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2000060-1
    ISSN 1943-7811 ; 1525-1578
    ISSN (online) 1943-7811
    ISSN 1525-1578
    DOI 10.1016/j.jmoldx.2018.10.009
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  7. Article: Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine.

    Tsai, Ellen A / Shakbatyan, Rimma / Evans, Jason / Rossetti, Peter / Graham, Chet / Sharma, Himanshu / Lin, Chiao-Feng / Lebo, Matthew S

    Journal of personalized medicine

    2016  Volume 6, Issue 1

    Abstract: Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient's genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence ... ...

    Abstract Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient's genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.
    Language English
    Publishing date 2016-02-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm6010012
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  8. Article ; Online: Corrigendum to: Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People.

    Lo, Yun-Hua / Cheng, Hsueh-Chien / Hsiung, Chia-Ni / Yang, Show-Ling / Wang, Han-Yu / Peng, Chia-Wei / Chen, Chun-Yu / Lin, Kung-Ping / Kang, Mei-Ling / Chen, Chien-Hsiun / Chu, Hou-Wei / Lin, Chiao-Feng / Lee, Mei-Hsuan / Liu, Quintin / Satta, Yoko / Lin, Cheng-Jui / Lin, Marie / Chaw, Shu-Miaw / Loo, Jun-Hun /
    Shen, Chen-Yang / Ko, Wen-Ya

    Molecular biology and evolution

    2021  Volume 38, Issue 10, Page(s) 4656

    Language English
    Publishing date 2021-08-20
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msab233
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  9. Article ; Online: Evolutionary dynamics of U12-type spliceosomal introns.

    Lin, Chiao-Feng / Mount, Stephen M / Jarmołowski, Artur / Makałowski, Wojciech

    BMC evolutionary biology

    2010  Volume 10, Page(s) 47

    Abstract: Background: Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) ... ...

    Abstract Background: Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.
    Results: We have investigated the evolution of U12-type introns among eighteen metazoan genomes by analyzing orthologous U12-type intron clusters. Examination of gain, loss, and type switching shows that intron type is remarkably conserved among vertebrates. Among 180 intron clusters, only eight show intron loss in any vertebrate species and only five show conversion between the U12 and the U2-type. Although there are only nineteen U12-type introns in Drosophila melanogaster, we found one case of U2 to U12-type conversion, apparently mediated by the activation of cryptic U12 splice sites early in the dipteran lineage. Overall, loss of U12-type introns is more common than conversion to U2-type and the U12 to U2 conversion occurs more frequently among introns of the GT-AG subtype than among introns of the AT-AC subtype. We also found support for natural U12-type introns with non-canonical terminal dinucleotides (CT-AC, GG-AG, and GA-AG) that have not been previously reported.
    Conclusions: Although complete loss of the U12-type spliceosome has occurred repeatedly, U12 introns are extremely stable in some taxa, including eutheria. Loss of U12 introns or the genes containing them is more common than conversion to the U2-type. The degeneracy of U12-type terminal dinucleotides among natural U12-type introns is higher than previously thought.
    MeSH term(s) Animals ; Arabidopsis/genetics ; Evolution, Molecular ; Humans ; Introns ; RNA, Small Nuclear/genetics ; Spliceosomes/genetics
    Chemical Substances RNA, Small Nuclear ; U12 small nuclear RNA
    Language English
    Publishing date 2010-02-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1471-2148
    ISSN (online) 1471-2148
    DOI 10.1186/1471-2148-10-47
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  10. Article ; Online: Birth and death of gene overlaps in vertebrates.

    Makałowska, Izabela / Lin, Chiao-Feng / Hernandez, Krisitina

    BMC evolutionary biology

    2007  Volume 7, Page(s) 193

    Abstract: Background: Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several ... ...

    Abstract Background: Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin.
    Results: Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap.
    Conclusion: Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.
    Language English
    Publishing date 2007-10-16
    Publishing country England
    Document type Journal Article
    ISSN 1471-2148
    ISSN (online) 1471-2148
    DOI 10.1186/1471-2148-7-193
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