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Article ; Online: Meeting the high expectations for liquid biopsy assays for pediatric brain tumors: Progress and challenges.

Biegel, Jaclyn A

2022 Volume 24, Issue 8, Page(s) 1364–1365

MeSH term(s)	Brain Neoplasms/diagnosis ; Cell-Free Nucleic Acids ; Child ; Genomics ; Humans ; Liquid Biopsy ; Motivation
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2022-04-05
Publishing country	England
Document type	Editorial ; Comment
ZDB-ID	2028601-6
ISSN	1523-5866 ; 1522-8517
ISSN (online)	1523-5866
ISSN	1522-8517
DOI	10.1093/neuonc/noac083
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Article ; Online: Novel

Hiemenz, Matthew C / Skrypek, Mary M / Cotter, Jennifer A / Biegel, Jaclyn A

JCO precision oncology

2022 Volume 3, Page(s) 1–6

Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.18.00385
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Article ; Online: Disease Evolution Monitored by Serial Cerebrospinal Fluid Liquid Biopsies in Two Cases of Recurrent Medulloblastoma.

O'Halloran, Katrina / Margol, Ashley / Davidson, Tom B / Estrine, Dolores / Tamrazi, Benita / Cotter, Jennifer A / Ji, Jianling / Biegel, Jaclyn A

International journal of molecular sciences

2024 Volume 25, Issue 9

Abstract: Medulloblastoma is the most common malignant brain tumor in childhood. Initial treatment generally includes surgery, irradiation, and chemotherapy. Approximately 20-30% of patients will experience a recurrence, which portends a very poor prognosis. The ... ...

Abstract	Medulloblastoma is the most common malignant brain tumor in childhood. Initial treatment generally includes surgery, irradiation, and chemotherapy. Approximately 20-30% of patients will experience a recurrence, which portends a very poor prognosis. The current standard of care for evaluation for relapse includes radiographic surveillance with magnetic resonance imaging at regular intervals. The presence of circulating tumor DNA in the cerebrospinal fluid has been demonstrated to be a predictor of a higher risk of progression in a research setting for patients with medulloblastoma treated on a prospective single institution clinical trial. We have previously published and clinically validated a liquid-biopsy-based genetic assay utilizing low-pass whole genome sequencing to detect copy number alterations in circulating tumor DNA. Here, we present two teenage patients with posterior fossa medulloblastoma with recurrent disease who have been monitored with serial liquid biopsies showing tumor evolution over time, demonstrating the clinical utility of these approaches.
MeSH term(s)	Humans ; Medulloblastoma/cerebrospinal fluid ; Medulloblastoma/genetics ; Medulloblastoma/diagnosis ; Medulloblastoma/pathology ; Medulloblastoma/diagnostic imaging ; Liquid Biopsy/methods ; Neoplasm Recurrence, Local/cerebrospinal fluid ; Neoplasm Recurrence, Local/genetics ; Adolescent ; Cerebellar Neoplasms/cerebrospinal fluid ; Cerebellar Neoplasms/diagnosis ; Cerebellar Neoplasms/pathology ; Cerebellar Neoplasms/genetics ; Male ; Circulating Tumor DNA/cerebrospinal fluid ; Circulating Tumor DNA/genetics ; Circulating Tumor DNA/blood ; Female ; Disease Progression ; Magnetic Resonance Imaging
Chemical Substances	Circulating Tumor DNA
Language	English
Publishing date	2024-04-30
Publishing country	Switzerland
Document type	Case Reports ; Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25094882
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Article ; Online: The genomic landscape of pediatric cancers: Implications for diagnosis and treatment.

Sweet-Cordero, E Alejandro / Biegel, Jaclyn A

Science (New York, N.Y.)

2019 Volume 363, Issue 6432, Page(s) 1170–1175

Abstract: The past decade has witnessed a major increase in our understanding of the genetic underpinnings of childhood cancer. Genomic sequencing studies have highlighted key differences between pediatric and adult cancers. Whereas many adult cancers are ... ...

Abstract	The past decade has witnessed a major increase in our understanding of the genetic underpinnings of childhood cancer. Genomic sequencing studies have highlighted key differences between pediatric and adult cancers. Whereas many adult cancers are characterized by a high number of somatic mutations, pediatric cancers typically have few somatic mutations but a higher prevalence of germline alterations in cancer predisposition genes. Also noteworthy is the remarkable heterogeneity in the types of genetic alterations that likely drive the growth of pediatric cancers, including copy number alterations, gene fusions, enhancer hijacking events, and chromoplexy. Because most studies have genetically profiled pediatric cancers only at diagnosis, the mechanisms underlying tumor progression, therapy resistance, and metastasis remain poorly understood. We discuss evidence that points to a need for more integrative approaches aimed at identifying driver events in pediatric cancers at both diagnosis and relapse. We also provide an overview of key aspects of germline predisposition for cancer in this age group.
MeSH term(s)	Adult ; Child ; DNA Copy Number Variations ; Disease Progression ; Genes, Neoplasm ; Genetic Predisposition to Disease ; Genomics/methods ; Humans ; Mutation ; Neoplasm Metastasis ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/pathology ; Neoplasms/therapy ; Oncogene Fusion ; Recurrence
Language	English
Publishing date	2019-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaw3535
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Article ; Online: Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations.

Shen, Lishuang / Bard, Jennifer Dien / Triche, Timothy J / Judkins, Alexander R / Biegel, Jaclyn A / Gai, Xiaowu

Emerging microbes & infections

2021 Volume 10, Issue 1, Page(s) 1293–1299

Abstract: The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor-binding domain (RBD) of the Spike (S) protein, ...

Abstract	The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor-binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the US that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date, this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021, it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggest this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.
MeSH term(s)	Binding Sites ; Humans ; Models, Molecular ; Mutation ; Phylogeny ; Protein Domains ; Protein Structure, Tertiary ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Sequence Analysis, RNA ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; United States ; Viral Matrix Proteins/genetics ; Whole Genome Sequencing/methods
Chemical Substances	Spike Glycoprotein, Coronavirus ; Viral Matrix Proteins ; membrane protein, SARS-CoV-2 ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-06-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2021.1943540
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Article ; Online: Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications.

Shen, Lishuang / Bard, Jennifer Dien / Triche, Timothy J / Judkins, Alexander R / Biegel, Jaclyn A / Gai, Xiaowu

Emerging microbes & infections

2021 Volume 10, Issue 1, Page(s) 885–893

Abstract: Mutations in the SARS-CoV-2 Membrane (M) gene are relatively uncommon. The M gene encodes the most abundant viral structural protein, and is implicated in multiple viral functions, including initial attachment to the host cell via heparin sulphate ... ...

Abstract	Mutations in the SARS-CoV-2 Membrane (M) gene are relatively uncommon. The M gene encodes the most abundant viral structural protein, and is implicated in multiple viral functions, including initial attachment to the host cell via heparin sulphate proteoglycan, viral protein assembly in conjunction with the N and E genes, and enhanced glucose transport. We have identified a recent spike in the frequency of reported SARS-CoV-2 genomes carrying M gene mutations. This is associated with emergence of a new sub-B.1 clade, B.1.I82T, defined by the previously unreported M:I82T mutation within TM3, the third of three membrane spanning helices implicated in glucose transport. The frequency of this mutation increased in the USA from 0.014% in October 2020 to 1.62% in February 2021, a 116-fold change. While constituting 0.7% of the isolates overall, M:I82T sub-B.1 lineage accounted for 14.4% of B.1 lineage isolates in February 2021, similar to the rapid initial increase previously seen with the B.1.1.7 and B.1.429 lineages, which quickly became the dominant lineages in Europe and California over a period of several months. A similar increase in incidence was also noted in another related mutation, V70L, also within the TM2 transmembrane helix. These M mutations are associated with younger patient age (4.6 to 6.3 years). The rapid emergence of this B.1.I82T clade, recently named Pangolin B.1.575 lineage, suggests that this M gene mutation is more biologically fit, perhaps related to glucose uptake during viral replication, and should be included in ongoing genomic surveillance efforts and warrants further evaluation for potentially increased pathogenic and therapeutic implications.
MeSH term(s)	Adult ; COVID-19/virology ; Cell Lineage ; Child ; Child, Preschool ; Humans ; Mutation ; Phylogeny ; SARS-CoV-2/genetics ; Viral Matrix Proteins/genetics
Chemical Substances	Viral Matrix Proteins ; membrane protein, SARS-CoV-2
Language	English
Publishing date	2021-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2021.1922097
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Article ; Online: Characterization of PAX5 intragenic tandem multiplication in pediatric B-lymphoblastic leukemia by optical genome mapping.

Jean, Jeffrey / Kovach, Alexandra E / Doan, Andrew / Oberley, Matthew / Ji, Jianling / Schmidt, Ryan J / Biegel, Jaclyn A / Bhojwani, Deepa / Raca, Gordana

Blood advances

2022 Volume 6, Issue 11, Page(s) 3343–3346

MeSH term(s)	Child ; Chromosome Mapping ; Humans ; Lymphoma, Non-Hodgkin ; PAX5 Transcription Factor/genetics ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
Chemical Substances	PAX5 Transcription Factor ; PAX5 protein, human
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2021006328
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Zs.A 7153: Show issues

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Article ; Online: Pediatric Chordoma: A Tale of Two Genomes.

O'Halloran, Katrina / Hakimjavadi, Hesamedin / Bootwalla, Moiz / Ostrow, Dejerianne / Kerawala, Rhea / Cotter, Jennifer A / Yellapantula, Venkata / Kaneva, Kristiyana / Wadhwani, Nitin R / Treece, Amy / Foreman, Nicholas K / Alexandrescu, Sanda / Velazquez Vega, Jose / Biegel, Jaclyn A / Gai, Xiaowu

Molecular cancer research : MCR

2024

Abstract: Little is known regarding the genomic alterations in chordoma, with the exception of loss of SMARCB1, a core member of the SWI/SNF complex, in poorly differentiated chordomas. A TBXT duplication and rs2305089 polymorphism, located at 6q27, are known ... ...

Abstract	Little is known regarding the genomic alterations in chordoma, with the exception of loss of SMARCB1, a core member of the SWI/SNF complex, in poorly differentiated chordomas. A TBXT duplication and rs2305089 polymorphism, located at 6q27, are known genetic susceptibility loci. A comprehensive genomic analysis of the nuclear and mitochondrial genomes in pediatric chordoma has not yet been reported. In this study, we performed whole exome and mitochondrial DNA (mtDNA) genome sequencing on 29 chordomas from 23 pediatric patients. Findings were compared with that from whole genome sequencing datasets of 80 adult skull base chordoma patients. In the pediatric chordoma cohort, 81% percent of the somatic mtDNA mutations were observed in NADH complex genes, which is significantly enriched compared to the rest of the mtDNA genes (p=0.001). In adult chordomas, mtDNA mutations were also enriched in the NADH complex genes (p<0.0001). Furthermore, a progressive increase in heteroplasmy of non-synonymous mtDNA mutations was noted in patients with multiple tumors (p=0.0007). In the nuclear genome, rare likely germline in-frame indels in ARID1B, a member of the SWI/SNF complex located at 6q25.3, were observed in five pediatric patients (22%) and four patients in the adult cohort (5%). The frequency of rare ARID1B indels in the pediatric cohort is significantly higher than that of the adult cohort (p=0.0236, Fisher's exact test), but they were both significantly higher than that in the ethnicity-matched populations (p<5.9e-07 and p<0.0001174, respectively). Implications: germline ARID1B indels and mtDNA aberrations appear important for chordoma genesis, especially in pediatric chordoma.
Language	English
Publishing date	2024-05-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2098788-2
ISSN	1557-3125 ; 1541-7786
ISSN (online)	1557-3125
ISSN	1541-7786
DOI	10.1158/1541-7786.MCR-23-0741
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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: Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country.

Shen, Lishuang / Dien Bard, Jennifer / Biegel, Jaclyn A / Judkins, Alexander R / Gai, Xiaowu

Frontiers in microbiology

2020 Volume 11, Page(s) 573430

Abstract: Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the ... ...

Abstract	Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions. This points to the effectiveness of existing travel restriction policies and public health measures in reducing the transmission of SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-09-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.573430
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