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Browsing by Author "Hodge, Jennelle C."
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Item A cross-disorder dosage sensitivity map of the human genome(Elsevier, 2022) Collins, Ryan L.; Glessner, Joseph T.; Porcu, Eleonora; Lepamets, Maarja; Brandon, Rhonda; Lauricella, Christopher; Han, Lide; Morley, Theodore; Niestroj, Lisa-Marie; Ulirsch, Jacob; Everett, Selin; Howrigan, Daniel P.; Boone, Philip M.; Fu, Jack; Karczewski, Konrad J.; Kellaris, Georgios; Lowther, Chelsea; Lucente, Diane; Mohajeri, Kiana; Nõukas, Margit; Nuttle, Xander; Samocha, Kaitlin E.; Trinh, Mi; Ullah, Farid; Võsa, Urmo; Epi25 Consortium; Estonian Biobank Research Team; Hurles, Matthew E.; Aradhya, Swaroop; Davis, Erica E.; Finucane, Hilary; Gusella, James F.; Janze, Aura; Katsanis, Nicholas; Matyakhina, Ludmila; Neale, Benjamin M.; Sanders, David; Warren, Stephanie; Hodge, Jennelle C.; Lal, Dennis; Ruderfer, Douglas M.; Meck, Jeanne; Mägi, Reedik; Esko, Tõnu; Reymond, Alexandre; Kutalik, Zoltán; Hakonarson, Hakon; Sunyaev, Shamil; Brand, Harrison; Talkowski, Michael E.; Medical and Molecular Genetics, School of MedicineRare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. In this study, we aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome. We harmonized and meta-analyzed rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene dense and often harbored dominant dosage sensitive driver genes, which we were able to prioritize using statistical fine-mapping. Finally, we designed an ensemble machine-learning model to predict probabilities of dosage sensitivity (pHaplo & pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. This dosage sensitivity resource will provide broad utility for human disease research and clinical genetics.Item A Multicenter Analysis of Abnormal Chromosomal Microarray Findings in Congenital Heart Disease(American Heart Association, 2023) Landis, Benjamin J.; Helvaty, Lindsey R.; Geddes, Gabrielle C.; Lin, Jiuann-Huey Ivy; Yatsenko, Svetlana A.; Lo, Cecilia W.; Border, William L.; Burns Wechsler, Stephanie; Murali, Chaya N.; Azamian, Mahshid S.; Lalani, Seema R.; Hinton, Robert B.; Garg, Vidu; McBride, Kim L.; Hodge, Jennelle C.; Ware, Stephanie M.; Pediatrics, School of MedicineBackground: Chromosomal microarray analysis (CMA) provides an opportunity to understand genetic causes of congenital heart disease (CHD). The methods for describing cardiac phenotypes in patients with CMA abnormalities have been inconsistent, which may complicate clinical interpretation of abnormal testing results and hinder a more complete understanding of genotype–phenotype relationships. Methods and Results: Patients with CHD and abnormal clinical CMA were accrued from 9 pediatric cardiac centers. Highly detailed cardiac phenotypes were systematically classified and analyzed for their association with CMA abnormality. Hierarchical classification of each patient into 1 CHD category facilitated broad analyses. Inclusive classification allowing multiple CHD types per patient provided sensitive descriptions. In 1363 registry patients, 28% had genomic disorders with well‐recognized CHD association, 67% had clinically reported copy number variants (CNVs) with rare or no prior CHD association, and 5% had regions of homozygosity without CNV. Hierarchical classification identified expected CHD categories in genomic disorders, as well as uncharacteristic CHDs. Inclusive phenotyping provided sensitive descriptions of patients with multiple CHD types, which occurred commonly. Among CNVs with rare or no prior CHD association, submicroscopic CNVs were enriched for more complex types of CHD compared with large CNVs. The submicroscopic CNVs that contained a curated CHD gene were enriched for left ventricular obstruction or septal defects, whereas CNVs containing a single gene were enriched for conotruncal defects. Neuronal‐related pathways were over‐represented in single‐gene CNVs, including top candidate causative genes NRXN3, ADCY2, and HCN1. Conclusions: Intensive cardiac phenotyping in multisite registry data identifies genotype–phenotype associations in CHD patients with abnormal CMA.Item Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms(Elsevier, 2018) Kanagal-Shamanna, Rashmi; Hodge, Jennelle C.; Tucker, Tracy; Shetty, Shashi; Yenamandra, Ashwini; Dixon-McIver, Amanda; Bryke, Christine; Huxley, Emma; Lennon, Patrick A.; Raca, Gordana; Xu, Xinjie; Jeffries, Sally; Quintero-Rivera, Fabiola; Greipp, Patricia T.; Slovak, Marilyn L.; Iqbal, M. Anwar; Fang, Min; Medical and Molecular Genetics, School of MedicineMultiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).Item Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group(Elsevier, 2018) Xu, Xinjie; Bryke, Christine; Sukhanova, Madina; Huxley, Emma; Dash, D. P.; Dixon-Mciver, Amanda; Fang, Min; Griepp, Patricia T.; Hodge, Jennelle C.; Iqbal, Anwar; Jeffries, Sally; Kanagal-Shamanna, Rashmi; Quintero-Rivera, Fabiola; Shetty, Shashi; Slovak, Marilyn L.; Yenamandra, Ashwini; Lennon, Patrick A.; Raca, Gordana; Medical and Molecular Genetics, School of MedicineStructural genomic abnormalities, including balanced chromosomal rearrangements, copy number gains and losses and copy-neutral loss-of-heterozygosity (CN-LOH) represent an important category of diagnostic, prognostic and therapeutic markers in acute myeloid leukemia (AML). Genome-wide evaluation for copy number abnormalities (CNAs) is at present performed by karyotype analysis which has low resolution and is unobtainable in a subset of cases. Furthermore, examination for possible CN-LOH in leukemia cells is at present not routinely performed in the clinical setting. Chromosomal microarray (CMA) analysis is a widely available assay for CNAs and CN-LOH in diagnostic laboratories, but there are currently no guidelines how to best incorporate this technology into clinical testing algorithms for neoplastic diseases including AML. The Cancer Genomics Consortium Working Group for Myeloid Neoplasms performed an extensive review of peer-reviewed publications focused on CMA analysis in AML. Here we summarize evidence regarding clinical utility of CMA analysis in AML extracted from published data, and provide recommendations for optimal utilization of CMA testing in the diagnostic workup. In addition, we provide a list of CNAs and CN-LOH regions which have documented clinical significance in diagnosis, prognosis and treatment decisions in AML.Item Computational pharmacogenotype extraction from clinical next-generation sequencing(Frontiers Media, 2023-07-04) Shugg, Tyler; Ly, Reynold C.; Osei, Wilberforce; Rowe, Elizabeth J.; Granfield, Caitlin A.; Lynnes, Ty C.; Medeiros, Elizabeth B.; Hodge, Jennelle C.; Breman, Amy M.; Schneider, Bryan P.; Sahinalp, S. Cenk; Numanagić, Ibrahim; Salisbury, Benjamin A.; Bray, Steven M.; Ratcliff, Ryan; Skaar, Todd C.; Medicine, School of MedicineBackground: Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively. Methods: Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1. Results: Mean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort. Conclusion: Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.Item A new microdeletion syndrome involving TBC1D24, ATP6V0C, and PDPK1 causes epilepsy, microcephaly, and developmental delay(Nature, 2018) Mucha, Bettina E.; Banka, Siddhart; Ajeawung, Norbert Fonya; Molidperee, Sirinart; Chen, Gary G.; Koenig, Mary Kay; Adejumo, Rhamat B.; Till, Marianne; Harbord, Michael; Perrier, Renee; Lemyre, Emmanuelle; Boucher, Renee-Myriam; Skotko, Brian G.; Waxler, Jessica L.; Thomas, Mary Ann; Hodge, Jennelle C.; Gecz, Jozef; Nicholl, Jillian; McGregor, Lesley; Linden, Tobias; Sisodiya, Sanjay M.; Sanlaville, Damien; Cheung, Sau W.; Ernst, Carl; Campeau, Philippe M.; Medical and Molecular Genetics, School of MedicinePurpose Contiguous gene deletions are known to cause several neurodevelopmental syndromes, many of which are caused by recurrent events on chromosome 16. However, chromosomal microarray studies (CMA) still yield copy-number variants (CNVs) of unknown clinical significance. We sought to characterize eight individuals with overlapping 205-kb to 504-kb 16p13.3 microdeletions that are distinct from previously published deletion syndromes. Methods Clinical information on the patients and bioinformatic scores for the deleted genes were analyzed. Results All individuals in our cohort displayed developmental delay, intellectual disability, and various forms of seizures. Six individuals were microcephalic and two had strabismus. The deletion was absent in all 13 parents who were available for testing. The area of overlap encompasses seven genes including TBC1D24, ATP6V0C, and PDPK1 (also known as PDK1). Bi-allelic TBC1D24 pathogenic variants are known to cause nonsyndromic deafness, epileptic disorders, or DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation, seizures). Sanger sequencing of the nondeleted TBC1D24 allele did not yield any additional pathogenic variants. Conclusions We propose that 16p13.3 microdeletions resulting in simultaneous haploinsufficiencies of TBC1D24, ATP6V0C, and PDPK1 cause a novel rare contiguous gene deletion syndrome of microcephaly, developmental delay, intellectual disability, and epilepsy.Item Non-Fusion Mutations in Endometrial Stromal Sarcomas: What is the Potential Impact on Tumorigenesis through Cell Cycle Dysregulation?(BMJ, 2020) Patel, Snehal B.; McCormack, Colin; Hodge, Jennelle C.; Medical and Molecular Genetics, School of MedicineTargeted next-generation sequencing using the 50-gene Ion AmpliSeq Cancer Hotspot Panel v2 identified two significant point mutations in endometrial stromal sarcomas (ESS). Case 1 is a uterine mass from a quadragenarian woman with a karyotype lacking any known ESS rearrangements but demonstrated to have a CTNNB1-activating mutation (c.133T>C, p.[Ser45Pro]). Analysis of a uterine mass from case 2, a sexagenarian woman, revealed biallelic CDKN2A-inactivating mutations (c.172C>T, p.[Arg58Ter] and a deletion). Break-apart studies to identify YWHAE, JAZF1 and PHF1 rearrangements were negative in both tumours. We propose a model in which these point mutations may affect cell proliferation, converging at Wnt signalling and G1-S checkpoint control, that independently or in concert with a rare gene fusion result in ESS tumour development or progression.Item Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies(Elsevier, 2023) Lowther, Chelsea; Valkanas, Elise; Giordano, Jessica L.; Wang, Harold Z.; Currall, Benjamin B.; O'Keefe, Kathryn; Pierce-Hoffman, Emma; Kurtas, Nehir E.; Whelan, Christopher W.; Hao, Stephanie P.; Weisburd, Ben; Jalili, Vahid; Fu, Jack; Wong, Isaac; Collins, Ryan L.; Zhao, Xuefang; Austin-Tse, Christina A.; Evangelista, Emily; Lemire, Gabrielle; Aggarwal, Vimla S.; Lucente, Diane; Gauthier, Laura D.; Tolonen, Charlotte; Sahakian, Nareh; Stevens, Christine; An, Joon-Yong; Dong, Shan; Norton, Mary E.; MacKenzie, Tippi C.; Devlin, Bernie; Gilmore, Kelly; Powell, Bradford C.; Brandt, Alicia; Vetrini, Francesco; DiVito, Michelle; Sanders, Stephan J.; MacArthur, Daniel G.; Hodge, Jennelle C.; O'Donnell-Luria, Anne; Rehm, Heidi L.; Vora, Neeta L.; Levy, Brynn; Brand, Harrison; Wapner, Ronald J.; Talkowski, Michael E.; Medical and Molecular Genetics, School of MedicineShort-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.Item The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Myeloid and Histiocytic/Dendritic Neoplasms(Springer, 2022) Khoury, Joseph D.; Solary, Eric; Abla, Oussama; Akkari, Yassmine; Alaggio, Rita; Apperley, Jane F.; Bejar, Rafael; Berti, Emilio; Busque, Lambert; Chan, John K. C.; Chen, Weina; Chen, Xueyan; Chng, Wee-Joo; Choi, John K.; Colmenero, Isabel; Coupland, Sarah E.; Cross, Nicholas C. P.; De Jong, Daphne; Elghetany, M. Tarek; Takahashi, Emiko; Emile, Jean-Francois; Ferry, Judith; Fogelstrand, Linda; Fontenay, Michaela; Germing, Ulrich; Gujral, Sumeet; Haferlach, Torsten; Harrison, Claire; Hodge, Jennelle C.; Hu, Shimin; Jansen, Joop H.; Kanagal-Shamanna, Rashmi; Kantarjian, Hagop M.; Kratz, Christian P.; Li, Xiao-Qiu; Lim, Megan S.; Loeb, Keith; Loghavi, Sanam; Marcogliese, Andrea; Meshinchi, Soheil; Michaels, Phillip; Naresh, Kikkeri N.; Natkunam, Yasodha; Nejati, Reza; Ott, German; Padron, Eric; Patel, Keyur P.; Patkar, Nikhil; Picarsic, Jennifer; Platzbecker, Uwe; Roberts, Irene; Schuh, Anna; Sewell, William; Siebert, Reiner; Tembhare, Prashant; Tyner, Jeffrey; Verstovsek, Srdan; Wang, Wei; Wood, Brent; Xiao, Wenbin; Yeung, Cecilia; Hochhaus, Andreas; Medical and Molecular Genetics, School of MedicineThe upcoming 5th edition of the World Health Organization (WHO) Classification of Haematolymphoid Tumours is part of an effort to hierarchically catalogue human cancers arising in various organ systems within a single relational database. This paper summarizes the new WHO classification scheme for myeloid and histiocytic/dendritic neoplasms and provides an overview of the principles and rationale underpinning changes from the prior edition. The definition and diagnosis of disease types continues to be based on multiple clinicopathologic parameters, but with refinement of diagnostic criteria and emphasis on therapeutically and/or prognostically actionable biomarkers. While a genetic basis for defining diseases is sought where possible, the classification strives to keep practical worldwide applicability in perspective. The result is an enhanced, contemporary, evidence-based classification of myeloid and histiocytic/dendritic neoplasms, rooted in molecular biology and an organizational structure that permits future scalability as new discoveries continue to inexorably inform future editions.Item The 5th Edition of the World Health Organization Classification of Tumours of the Eye and Orbit(Karger, 2023) Milman, Tatyana; Grossniklaus, Hans E.; Goldman-Levy, Gabrielle; Kivelä, Tero T.; Coupland, Sarah E.; White, Valerie A.; Mudhar, Hardeep Singh; Eberhart, Charles G.; Verdijk, Robert M.; Heegaard, Steffen; Gill, Anthony J.; Jager, Martine J.; Rodríguez-Reyes, Abelardo A.; Esmaeli, Bita; Hodge, Jennelle C.; Cree, Ian A.; WHO Classification of Tumours Editorial Board; Medical and Molecular Genetics, School of Medicine