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Article ; Online: Significance Associated with Phenotype Score Aids in Variant Prioritization for Exome Sequencing Analysis.

Lee, Brian / Nasanovsky, Lily / Shen, Lishuang / Maglinte, Dennis T / Pan, Yachen / Gai, Xiaowu / Schmidt, Ryan J / Raca, Gordana / Biegel, Jaclyn A / Roytman, Megan / An, Paul / Saunders, Carol J / Farrow, Emily G / Shams, Soheil / Ji, Jianling

The Journal of molecular diagnostics : JMD

2024 Volume 26, Issue 5, Page(s) 337–348

Abstract: Several in silico annotation-based methods have been developed to prioritize variants in exome sequencing analysis. This study introduced a novel metric Significance Associated with Phenotypes (SAP) score, which generates a statistical score by comparing ...

Abstract	Several in silico annotation-based methods have been developed to prioritize variants in exome sequencing analysis. This study introduced a novel metric Significance Associated with Phenotypes (SAP) score, which generates a statistical score by comparing an individual's observed phenotypes against existing gene-phenotype associations. To evaluate the SAP score, a retrospective analysis was performed on 219 exomes. Among them, 82 family-based and 35 singleton exomes had at least one disease-causing variant that explained the patient's clinical features. SAP scores were calculated, and the rank of the disease-causing variant was compared with a known method, Exomiser. Using the SAP score, the known causative variant was ranked in the top 10 retained variants for 94% (77 of 82) of the family-based exomes and in first place for 73% of these cases. For singleton exomes, the SAP score analysis ranked the known pathogenic variants within the top 10 for 80% (28 of 35) of cases. The SAP score, which is independent of detected variants, demonstrates comparable performance with Exomiser, which considers both phenotype and variant-level evidence simultaneously. Among 102 cases with negative results or variants of uncertain significance, SAP score analysis revealed two cases with a potential new diagnosis based on rank. The SAP score, a phenotypic quantitative metric, can be used in conjunction with standard variant filtration and annotation to enhance variant prioritization in exome analysis.
MeSH term(s)	Humans ; Exome Sequencing ; Retrospective Studies ; Databases, Genetic ; Genetic Testing ; Phenotype
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2024.01.009
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Article ; Online: Utility of viral whole-genome sequencing for institutional infection surveillance during the coronavirus disease 2019 (COVID-19) pandemic.

Ryutov, Alex / Gai, Xiaowu / Ostrow, Dejerianne / Maglinte, Dennis T / Flores, Jessica / Salas, Edahrline J / Glucoft, Marisa / Smit, Michael / Dien Bard, Jennifer

Infection control and hospital epidemiology

2021 Volume 43, Issue 8, Page(s) 1086–1088

MeSH term(s)	COVID-19 ; Cross Infection ; Humans ; Infection Control ; Pandemics ; SARS-CoV-2/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2021-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2021.185
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Article ; Online: Implementation of a Streamlined SARS-CoV-2 Whole-Genome Sequencing Assay for Expeditious Surveillance during the Emergence of the Omicron Variant.

Fissel, John A / Mestas, Javier / Chen, Pei Ying / Flores-Vazquez, Jessica / Truong, Thao T / Bootwalla, Moiz / Maglinte, Dennis T / Gai, Xiaowu / Dien Bard, Jennifer

Journal of clinical microbiology

2022 Volume 60, Issue 4, Page(s) e0256921

MeSH term(s)	COVID-19 ; Humans ; Mutation ; SARS-CoV-2/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2022-03-23
Publishing country	United States
Document type	Letter
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.02569-21
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Article ; Online: Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory.

Ponomarenko, Petr / Ryutov, Alex / Maglinte, Dennis T / Baranova, Ancha / Tatarinova, Tatiana V / Gai, Xiaowu

BMC medical genomics

2017 Volume 10, Issue 1, Page(s) 57

Abstract: Background: With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an ... ...

Abstract	Background: With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, and provides cost-efficient means for determining gender, ethnic ancestry, and sample kinships, that are important for data interpretation of NGS-based genetic tests. Methods: We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing. Accuracy and robustness of determining gender, provenance, and kinships were assessed. Results: Concordance of genotype calls between Infinium QC and other platforms was above 99%. Here we show that the chip's ancestry informative markers are sufficient for ethnicity determination at continental and sometimes subcontinental levels, with assignment accuracy varying with the coverage for a particular region and ethnic groups. Mean accuracies of provenance prediction at a regional level were varied from 81% for Asia, to 89% for Americas, 86% for Africa, 97% for Oceania, 98% for Europe, and 100% for India. Mean accuracy of ethnicity assignment predictions was 63%. Pairwise concordances of AFR samples with the samples from any other super populations were the lowest (0.39-0.43), while the concordances within the same population were relatively high (0.55-0.61). For all populations except African, cross-population comparisons were similar in their concordance ranges to the range of within-population concordances (0.54-0.57). Gender determination was correct in all tested cases. Conclusions: Our results indicate that the Infinium QC Array-24 chip is suitable for cost-efficient, independent QC assaying in the settings of an NGS-based molecular diagnostic laboratory; hence, we recommend its integration into the standard laboratory workflow. Low-density chips can provide sample-specific measures for variant call accuracy, prevent sample mix-ups, validate self-reported ethnicities, and detect consanguineous cases. Integration of low-density chips into QC procedures aids proper interpretation of candidate sequence variants. To enhance utility of this low-density chip, we recommend expansion of ADME and mitochondrial markers. Inexpensive Infinium-like low-density human chips have a potential to become a "Swiss army knife" among genotyping assays suitable for many applications requiring high-throughput assays.
MeSH term(s)	Female ; Genomics/methods ; Genotyping Techniques/methods ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Molecular Diagnostic Techniques/methods ; Pedigree ; Reproducibility of Results ; Whole Exome Sequencing
Language	English
Publishing date	2017-10-06
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1755-8794
ISSN (online)	1755-8794
DOI	10.1186/s12920-017-0297-7
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Article: Early pandemic molecular diversity of SARS-CoV-2 in children.

Moustafa, Ahmed M / Otto, William / Gai, Xiaowu / Pandey, Utsav / Ryutov, Alex / Bootwalla, Moiz / Maglinte, Dennis T / Shen, Lishuang / Ruble, David / Ostrow, Dejerianne / Gerber, Jeffrey S / Bard, Jennifer Dien / Harris, Rebecca M / Planet, Paul J

medRxiv : the preprint server for health sciences

2021

Abstract: Background: In the US, community circulation of the SARS-CoV-2 virus likely began in February 2020 after mostly travel-related cases. Children's Hospital of Philadelphia began testing on 3/9/2020 for pediatric and adult patients, and for all admitted ... ...

Abstract	Background: In the US, community circulation of the SARS-CoV-2 virus likely began in February 2020 after mostly travel-related cases. Children's Hospital of Philadelphia began testing on 3/9/2020 for pediatric and adult patients, and for all admitted patients on 4/1/2020, allowing an early glimpse into the local molecular epidemiology of the virus. Methods: We obtained 169 SARS-CoV-2 samples (83 from patients <21 years old) from March through May and produced whole genome sequences. We used genotyping tools to track variants over time and to test for possible genotype associated clinical presentations and outcomes in children. Results: Our analysis uncovered 13 major lineages that changed in relative abundance as cases peaked in mid-April in Philadelphia. We detected at least 6 introductions of distinct viral variants into the population. As a group, children had more diverse virus genotypes than the adults tested. No strong differences in clinical variables were associated with genotypes. Conclusions: Whole genome analysis revealed unexpected diversity, and distinct circulating viral variants within the initial peak of cases in Philadelphia. Most introductions appeared to be local from nearby states. Although limited by sample size, we found no evidence that different genotypes had different clinical impacts in children in this study.
Language	English
Publishing date	2021-02-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.02.17.21251960
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Article ; Online: Mitochondrial DNA haplogroup, genetic ancestry, and susceptibility to Ewing sarcoma.

Kaneva, Kristiyana / Schurr, Theodore G / Tatarinova, Tatiana V / Buckley, Jonathan / Merkurjev, Daria / Triska, Petr / Liu, Xiyu / Done, James / Maglinte, Dennis T / Deapen, Dennis / Hwang, Amie / Schiffman, Joshua D / Triche, Timothy J / Biegel, Jaclyn A / Gai, Xiaowu

Mitochondrion

2022 Volume 67, Page(s) 6–14

Abstract: Based on current studies, the incidence of Ewing sarcoma (ES) varies significantly by race and ethnicity, with the disease being most common in patients of European ancestry. However, race/ethnicity has generally been self-reported rather than formally ... ...

Abstract	Based on current studies, the incidence of Ewing sarcoma (ES) varies significantly by race and ethnicity, with the disease being most common in patients of European ancestry. However, race/ethnicity has generally been self-reported rather than formally evaluated at a population level using DNA evidence. Additionally, mitochondrial dysfunction is a hallmark of ES, yet there have been no reported studies of mitochondrial genetics in ES. Thus, we evaluated both the mitochondrial and nuclear ancestries of 420 pediatric ES patients in the United States using whole-genome sequencing. We found that the mitochondrial DNA (mtDNA) genomes of only six (1.4 %) patients belonged to African L haplogroups, while those of 90 % of the patients belonged to macrohaplogroup R, which includes haplogroup H, the most common maternal lineage in Europe. Compared to the general US population, European haplogroups were significantly enriched in ES patients (p < 2.2e-16) and the African haplogroups are significantly impoverished (p < 4.6e-16). Using the ancestry informative markers defined in a National Genographic study, the vast majority of patients exhibited significant nuclear ancestry originating from the Mediterranean, Northern Europe, and Southwest Asia, including all six patients with African L mtDNAs. Very few had primarily African nuclear ancestry. This is the first genomic epidemiology study to simultaneously interrogate the mitochondrial and nuclear ancestries of ES patients. While supporting previous findings of enriched European ancestry in ES patients, these results also suggest alternative hypotheses for the significant contribution of mitochondrial ancestry in ES patients, as well as the protective role of African ancestry.
MeSH term(s)	Humans ; Child ; DNA, Mitochondrial/genetics ; Haplotypes ; Sarcoma, Ewing/genetics ; Black People ; Mitochondria/genetics
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2022-09-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2056923-3
ISSN	1872-8278 ; 1567-7249
ISSN (online)	1872-8278
ISSN	1567-7249
DOI	10.1016/j.mito.2022.09.002
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Article: High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19.

Pandey, Utsav / Yee, Rebecca / Shen, Lishuang / Judkins, Alexander R / Bootwalla, Moiz / Ryutov, Alex / Maglinte, Dennis T / Ostrow, Dejerianne / Precit, Mimi / Biegel, Jaclyn A / Bender, Jeffrey M / Gai, Xiaowu / Dien Bard, Jennifer

Open forum infectious diseases

2020 Volume 8, Issue 6, Page(s) ofaa551

Abstract: Background: The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical ... ...

Abstract	Background: The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children. Methods: Whole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity. Results: Higher viral load was detected in symptomatic patients ( Conclusions: Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.
Language	English
Publishing date	2020-11-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofaa551
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Article ; Online: Early pandemic molecular diversity of SARS-CoV-2 in children

medRxiv

Abstract: Background In the US, community circulation of the SARS-CoV-2 virus likely began in February 2020 after mostly travel-related cases. Children9s Hospital of Philadelphia began testing on 3/9/2020 for pediatric and adult patients, and for all admitted ... ...

Abstract	Background In the US, community circulation of the SARS-CoV-2 virus likely began in February 2020 after mostly travel-related cases. Children9s Hospital of Philadelphia began testing on 3/9/2020 for pediatric and adult patients, and for all admitted patients on 4/1/2020, allowing an early glimpse into the local molecular epidemiology of the virus. Methods We obtained 169 SARS-CoV-2 samples (83 from patients <21 years old) from March through May and produced whole genome sequences. We used genotyping tools to track variants over time and to test for possible genotype associated clinical presentations and outcomes in children. Results Our analysis uncovered 13 major lineages that changed in relative abundance as cases peaked in mid-April in Philadelphia. We detected at least 6 introductions of distinct viral variants into the population. As a group, children had more diverse virus genotypes than the adults tested. No strong differences in clinical variables were associated with genotypes. Conclusions Whole genome analysis revealed unexpected diversity, and distinct circulating viral variants within the initial peak of cases in Philadelphia. Most introductions appeared to be local from nearby states. Although limited by sample size, we found no evidence that different genotypes had different clinical impacts in children in this study.
Keywords	covid19
Language	English
Publishing date	2021-02-19
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.02.17.21251960
Database	COVID19

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Article ; Online: A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants.

Ji, Jianling / Shen, Lishuang / Bootwalla, Moiz / Quindipan, Catherine / Tatarinova, Tatiana / Maglinte, Dennis T / Buckley, Jonathan / Raca, Gordana / Saitta, Sulagna C / Biegel, Jaclyn A / Gai, Xiaowu

Cold Spring Harbor molecular case studies

2019 Volume 5, Issue 2

Abstract: Advancing the clinical utility of whole-exome sequencing (WES) for patients with suspected genetic disorders is largely driven by bioinformatics approaches that streamline data processing and analysis. Herein, we describe our experience with implementing ...

Abstract	Advancing the clinical utility of whole-exome sequencing (WES) for patients with suspected genetic disorders is largely driven by bioinformatics approaches that streamline data processing and analysis. Herein, we describe our experience with implementing a semiautomated and phenotype-driven WES diagnostic workflow, incorporating both the DRAGEN pipeline and the Exomiser variant prioritization tool, at an academic children's hospital with an ethnically diverse pediatric patient population. We achieved a 41% molecular diagnostic rate for 66 duo-, quad-, or trio-WES cases, and 28% for 40 singleton-WES cases. Preliminary results were returned to ordering physicians within 1 wk for 12 of 38 (32%) probands with positive findings, which were instrumental in guiding the appropriate clinical management for a variety of patients, especially in critical care settings. The semiautomated and streamlined WES workflow also enabled us to identify novel variants in candidate disease genes in patients with developmental delay and autism and immune disorders and cancer, including
MeSH term(s)	Adolescent ; Autism Spectrum Disorder/diagnosis ; Autism Spectrum Disorder/genetics ; Child ; Child, Preschool ; Early Diagnosis ; Female ; Genetic Predisposition to Disease ; Humans ; Immune System Diseases/diagnosis ; Immune System Diseases/genetics ; Infant ; Infant, Newborn ; Male ; Neoplasms/diagnosis ; Neoplasms/genetics ; Sensitivity and Specificity ; Time Factors ; Whole Exome Sequencing/methods ; Workflow ; Young Adult
Language	English
Publishing date	2019-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a003756
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Article ; Online: Pediatric COVID-19 in Southern California: clinical features and viral genetic diversity

Pandey, Utsav / Yee, Rebecca / Precit, Mimi / Bootwalla, Moiz / Ryutov, Alex / Shen, Lishuang / Maglinte, Dennis T / Ostrow, Dejerianne / Biegel, Jaclyn A / Judkins, Alexander R / Bender, Jeffrey M / Gai, Xiaowu / Dien Bard, Jennifer

medRxiv

Abstract: Clinical presentation of COVID-19 in children remains under investigation. In this manuscript, we present a summary of clinical findings from the first 23 cases of COVID-19 in children at Children9s Hospital Los Angeles. Considering the paucity of ... ...

Abstract	Clinical presentation of COVID-19 in children remains under investigation. In this manuscript, we present a summary of clinical findings from the first 23 cases of COVID-19 in children at Children9s Hospital Los Angeles. Considering the paucity of genomics data for circulating SARS-CoV-2 isolates in Southern California, we also present an overview of the viral genetic diversity in isolates obtained from these patients and compare them to isolates from other parts of the United States and globally. Our study presents much needed clinical and viral genomics data pertaining to COVID-19 in children.
Keywords	covid19
Language	English
Publishing date	2020-06-01
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.05.28.20104539
Database	COVID19

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