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Article ; Online: Epithelioid Angiomyolipoma With Prominent Papillary Architecture Mimicking Renal Cell Carcinoma: A Case Report.

Xiao, Andrew / Van Ziffle, Jessica / Chan, Emily

International journal of surgical pathology

2023 Volume 32, Issue 1, Page(s) 206–208

Abstract: Renal epithelioid angiomyolipoma (EAML) (epithelioid PEComa of the kidney), is a rare subtype of renal angiomyolipoma with the potential for aggressive behavior and a known diagnostically challenging entity. We present a renal EAML with unusual papillary ...

Abstract	Renal epithelioid angiomyolipoma (EAML) (epithelioid PEComa of the kidney), is a rare subtype of renal angiomyolipoma with the potential for aggressive behavior and a known diagnostically challenging entity. We present a renal EAML with unusual papillary architecture and tumor cells with abundant eosinophilic cytoplasm and cherry-red nucleoli with perinucleolar halos, strongly mimicking a fumarate hydratase (FH) deficient renal cell carcinoma (RCC). We herein report our findings and discuss the morphologic, immunohistochemical, and molecular pitfalls to consider in the differential of EAML, including with FH-deficient RCC and more recently described entities:
MeSH term(s)	Humans ; Carcinoma, Renal Cell/diagnosis ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; Kidney Neoplasms/diagnosis ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Angiomyolipoma/diagnosis ; Angiomyolipoma/pathology ; Biomarkers, Tumor ; Kidney/pathology ; Hamartoma
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2023-05-09
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	1336393-1
ISSN	1940-2465 ; 1066-8969
ISSN (online)	1940-2465
ISSN	1066-8969
DOI	10.1177/10668969231171942
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Article ; Online: TRAF7

Kaidonis, Georgia / Pekmezci, Melike / Van Ziffle, Jessica / Auguste, Kurtis I / Horton, Jonathan C

Journal of neurosurgery. Case lessons

2022 Volume 3, Issue 23, Page(s) CASE2247

Abstract: Background: In the past decade, next-generation sequencing has spurred significant progress in the understanding of cytogenetic alterations that occur in meningiomas. Eighty percent of adult meningiomas harbor pathogenic somatic variants involving : ... ...

Abstract	Background: In the past decade, next-generation sequencing has spurred significant progress in the understanding of cytogenetic alterations that occur in meningiomas. Eighty percent of adult meningiomas harbor pathogenic somatic variants involving Observations: This case involved a 15-year-old girl with bilateral optic nerve sheath meningiomas, diffuse meningiomatosis, and syndromic features, including craniosynostosis, brain anomalies, syndactyly, brachydactyly, epicanthus, and patent ductus arteriosus. Genetic testing of the meningioma specimen 7 years after biopsy showed a pathogenic p.R641C variant within the WD40 domain of the Lessons: The authors report postzygotic somatic mosaicism for a p.R641C variant in the
Language	English
Publishing date	2022-06-06
Publishing country	United States
Document type	Case Reports
ISSN	2694-1902
ISSN (online)	2694-1902
DOI	10.3171/CASE2247
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Article ; Online: Further description of two patients with biallelic variants in NADSYN1 in association with cardiac and vertebral anomalies.

Kortbawi, Hannah / Ames, Elizabeth / Pritchard, Amanda / Devine, Patrick / van Ziffle, Jessica / Slavotinek, Anne

American journal of medical genetics. Part A

2022 Volume 188, Issue 8, Page(s) 2479–2484

Abstract: Congenital nicotinamide adenine dinucleotide (NAD) deficiency disorders are associated with pathogenic variants in the genes NADSYN1, HAAO, and KYNU. These disorders overlap with the anomalies present in vertebral, anal, cardiac, tracheoesophageal, ... ...

Abstract	Congenital nicotinamide adenine dinucleotide (NAD) deficiency disorders are associated with pathogenic variants in the genes NADSYN1, HAAO, and KYNU. These disorders overlap with the anomalies present in vertebral, anal, cardiac, tracheoesophageal, radial and renal, and limb anomalies (VATER/VACTERL) association and often result in premature death. Children who survive typically have developmental delays or intellectual disability. Here, we describe two patients with compound heterozygous variants in NADSYN1 who presented with cardiac and vertebral defects overlapping with the VATER/VACTERL association, although the patients did not satisfy criteria for the diagnosis of VATER/VACTERL due to their lack of limb anomalies and significant renal anomalies. One patient survived into childhood with developmental delays and may represent an expansion of the survival data for NADSYN1-associated NAD deficiency disorders. Interestingly, one patient had hypoplastic left heart syndrome (HLHS) and one had an aortic coarctation and transverse hypoplasia of the aortic arch, suggesting that NADSYN1 sequencing should be performed in children presenting with congenital anomalies related to VATER/VACTERL association and with HLHS and aortic arch abnormalities.
MeSH term(s)	Abnormalities, Multiple ; Anal Canal/abnormalities ; Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor ; Child ; Esophagus/abnormalities ; Heart Defects, Congenital/complications ; Heart Defects, Congenital/diagnosis ; Heart Defects, Congenital/genetics ; Hernia, Diaphragmatic ; Humans ; Kidney/abnormalities ; Limb Deformities, Congenital/genetics ; NAD ; Spine/abnormalities ; Trachea/abnormalities
Chemical Substances	NAD (0U46U6E8UK) ; Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor (EC 6.3.5.-) ; NADSYN1 protein, human (EC 6.3.5.-)
Language	English
Publishing date	2022-05-02
Publishing country	United States
Document type	Case Reports
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.62765
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Zs.A 1376/A: Show issues

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Article ; Online: EML4::ALK fusions in complex lymphatic malformations.

Apsel Winger, Beth / Devine, Walter Patrick / Hsiao, Edward C / Zapala, Matthew / Van Ziffle, Jessica / Gupta, Nalin / Frieden, Ilona J / Shimano, Kristin A

Pediatric blood & cancer

2023 , Page(s) e30516

Abstract: Gorham-Stout disease (GSD) and generalized lymphatic anomaly (GLA) are subtypes of complex lymphatic malformations (CLMs) with osseous involvement that cause significant complications, including pain and pathologic fractures. As with other vascular ... ...

Abstract	Gorham-Stout disease (GSD) and generalized lymphatic anomaly (GLA) are subtypes of complex lymphatic malformations (CLMs) with osseous involvement that cause significant complications, including pain and pathologic fractures. As with other vascular anomalies, somatic mosaic mutations in oncogenes are often present, and the mTOR inhibitor sirolimus alleviates symptoms in some, but not all, patients. We describe two patients, one with GSD and one with GLA, found to have EML4::ALK fusions. This report of a targetable, oncogenic fusion in vascular malformations expands our understanding of the genetic basis for CLMs and suggests additional targeted therapies could be effective.
Language	English
Publishing date	2023-06-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2131448-2
ISSN	1545-5017 ; 1545-5009
ISSN (online)	1545-5017
ISSN	1545-5009
DOI	10.1002/pbc.30516
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Article ; Online: Genetic ancestry and diagnostic yield of exome sequencing in a diverse population.

Mavura, Yusuph / Sahin-Hodoglugil, Nuriye / Hodoglugil, Ugur / Kvale, Mark / Martin, Pierre-Marie / Van Ziffle, Jessica / Devine, W Patrick / Ackerman, Sara L / Koenig, Barbara A / Kwok, Pui-Yan / Norton, Mary E / Slavotinek, Anne / Risch, Neil

NPJ genomic medicine

2024 Volume 9, Issue 1, Page(s) 1

Abstract: It has been suggested that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental/subcontinental genetic ... ...

Abstract	It has been suggested that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental/subcontinental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Cases (N = 845) with suspected genetic disorders underwent ES for diagnosis. Continental/subcontinental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov-Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. We observed no reduction in overall DY associated with any genetic ancestry (African, Native American, East Asian, European, Middle Eastern, South Asian). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2813848-X
ISSN	2056-7944 ; 2056-7944
ISSN (online)	2056-7944
ISSN	2056-7944
DOI	10.1038/s41525-023-00385-6
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Article ; Online: A missense variant, p.(Ile269Asn), in MC4R as a secondary finding in a child with BCL11A-related intellectual disability.

Beleford, Daniah T / Van Ziffle, Jessica / Hodoglugil, Ugur / Slavotinek, Anne M

European journal of medical genetics

2020 Volume 63, Issue 9, Page(s) 103969

Abstract: We describe a three year old female who underwent clinical exome sequencing and was diagnosed with BCL11A-related intellectual disability/Dias-Logan syndrome due to a de novo, heterozygous variant in the BCL11A gene, NM_018014.3:c.148C > T; p.(Gln50*). A ...

Abstract	We describe a three year old female who underwent clinical exome sequencing and was diagnosed with BCL11A-related intellectual disability/Dias-Logan syndrome due to a de novo, heterozygous variant in the BCL11A gene, NM_018014.3:c.148C > T; p.(Gln50*). A missense variant in MC4R, NM_005912.3:c.806T > A; p.(Ile269Asn), was also reported as a secondary finding. In her family, her father, paternal aunt, and paternal uncle were all reported to have height and weight measurements suggestive of Class 3 obesity with BMI>40 kg/m
MeSH term(s)	Child, Preschool ; Developmental Disabilities/genetics ; Developmental Disabilities/pathology ; Female ; Humans ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; Mutation, Missense ; Receptor, Melanocortin, Type 4/genetics ; Repressor Proteins/genetics
Chemical Substances	BCL11A protein, human ; MC4R protein, human ; Receptor, Melanocortin, Type 4 ; Repressor Proteins
Language	English
Publishing date	2020-06-10
Publishing country	Netherlands
Document type	Case Reports ; Letter
ZDB-ID	2184135-4
ISSN	1878-0849 ; 1769-7212
ISSN (online)	1878-0849
ISSN	1769-7212
DOI	10.1016/j.ejmg.2020.103969
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Article ; Online: Checkpoint Inhibitor Immunotherapy to Treat Temozolomide-Associated Hypermutation in Advanced Atypical Carcinoid Tumor of the Lung.

Sun, Fangdi / Grenert, James P / Tan, Lisa / Van Ziffle, Jessica / Joseph, Nancy M / Mulvey, Claire K / Bergsland, Emily

JCO precision oncology

2022 Volume 6, Page(s) e2200009

MeSH term(s)	Carcinoid Tumor/drug therapy ; Humans ; Immunotherapy/adverse effects ; Lung Neoplasms/drug therapy ; Temozolomide/therapeutic use
Chemical Substances	Temozolomide (YF1K15M17Y)
Language	English
Publishing date	2022-06-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.22.00009
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Article ; Online: The utility of pathologic examination and comprehensive phenotyping for accurate diagnosis with perinatal exome sequencing.

Swanson, Kate / Norton, Mary E / Lianoglou, Billie R / Jelin, Angie C / Hodoglugil, Ugur / Van Ziffle, Jessica / Devine, Patrick / Sparks, Teresa N

Prenatal diagnosis

2022 Volume 42, Issue 10, Page(s) 1288–1294

Abstract: Objective: Exome sequencing (ES) offers the ability to assess for variants in thousands of genes and is particularly useful in the setting of fetal anomalies. However, the ES pipeline relies on a thorough understanding of an individual patient's ... ...

Abstract	Objective: Exome sequencing (ES) offers the ability to assess for variants in thousands of genes and is particularly useful in the setting of fetal anomalies. However, the ES pipeline relies on a thorough understanding of an individual patient's phenotype, which may be limited in the prenatal setting. Additional pathology evaluations in the pre- and postnatal settings can add phenotypic details important for clearly establishing and characterizing a diagnosis. Methods: This is a case series of prenatal ES performed at our institution in which pathology evaluations, including autopsy, dysmorphology examination, histology, and peripheral blood smear, augmented the understanding of the fetal phenotype. ES was performed at our institution and a multidisciplinary panel reviewed and classified the variants for each case. Results: We present four cases wherein pathology evaluations were beneficial for supporting a perinatal diagnosis identified with ES. In each of these cases, pathology findings provided additional data to support a more complete understanding of the relationship between the perinatal phenotype and variants identified with ES. Conclusion: These cases highlight challenges of perinatal ES related to incomplete prenatal phenotyping, demonstrate the utility of pathology evaluations to support diagnoses identified with ES, and further characterize the disease manifestations of specific genetic variants.
MeSH term(s)	Exome ; Female ; Fetus/diagnostic imaging ; Humans ; Pregnancy ; Prenatal Diagnosis ; Ultrasonography, Prenatal ; Exome Sequencing
Language	English
Publishing date	2022-07-03
Publishing country	England
Document type	Journal Article
ZDB-ID	82031-3
ISSN	1097-0223 ; 0197-3851
ISSN (online)	1097-0223
ISSN	0197-3851
DOI	10.1002/pd.6197
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Zs.A 1625: Show issues

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Article: Diagnostic Yield of Exome Sequencing in a Diverse Pediatric and Prenatal Population is not Associated with Genetic Ancestry.

medRxiv : the preprint server for health sciences

2023

Abstract: Purpose: It has been hypothesized that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental genetic ... ...

Abstract	Purpose: It has been hypothesized that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Methods: Cases (N=845) with suspected genetic disorders underwent ES for diagnosis. Continental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. Results: We observed no reduction in overall DY associated with any continental genetic ancestry (Africa, America, East Asia, Europe, Middle East, South Asia). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. Conclusions: In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the ethical and equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.
Language	English
Publishing date	2023-05-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.19.23290066
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Article: TFG::ALK

Xiao, Andrew / Shahmarvand, Nahid / Nagy, Alexandra / Kumar, Jyoti / Van Ziffle, Jessica / Devine, Patrick / Huang, Franklin / Lezama, Lhara / Li, Peng / Ohgami, Robert S

Frontiers in oncology

2023 Volume 13, Page(s) 1174606

Abstract: Anaplastic lymphoma kinase (ALK) positive large B-cell lymphoma (ALK+ LBCL) is an aggressive and rare subtype of B-cell lymphoma. Patients typically present with advanced clinical stage disease and do not respond to conventional chemotherapy; the median ... ...

Abstract	Anaplastic lymphoma kinase (ALK) positive large B-cell lymphoma (ALK+ LBCL) is an aggressive and rare subtype of B-cell lymphoma. Patients typically present with advanced clinical stage disease and do not respond to conventional chemotherapy; the median overall survival is 1.8 years. The genetic landscape of this entity remains poorly understood. Here we report a unique case of ALK+ LBCL harbouring a rare
Language	English
Publishing date	2023-05-25
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1174606
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