Browsing by Subject "Next-generation sequencing"
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Item Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping(Elsevier, 2018-04) Ridge, Perry G.; Wadsworth, Mark E.; Miller, Justin B.; Saykin, Andrew J.; Green, Robert C.; Alzheimer’s Disease Neuroimaging Initiative; Kauwe, John S. K.; Radiology and Imaging Sciences, School of MedicineINTRODUCTION: Mitochondrial genetics are an important but largely neglected area of research in Alzheimer's disease. A major impediment is the lack of data sets. METHODS: We used an innovative, rigorous approach, combining several existing tools with our own, to accurately assemble and call variants in 809 whole mitochondrial genomes. RESULTS: To help address this impediment, we prepared a data set that consists of 809 complete and annotated mitochondrial genomes with samples from the Alzheimer's Disease Neuroimaging Initiative. These whole mitochondrial genomes include rich phenotyping, such as clinical, fluid biomarker, and imaging data, all of which is available through the Alzheimer's Disease Neuroimaging Initiative website. Genomes are cleaned, annotated, and prepared for analysis. DISCUSSION: These data provide an important resource for investigating the impact of mitochondrial genetic variation on risk for Alzheimer's disease and other phenotypes that have been measured in the Alzheimer's Disease Neuroimaging Initiative samples.Item Clinical benefit of a precision medicine based approach for guiding treatment of refractory cancers(Impact Journals, 2016-08-30) Radovich, Milan; Kiel, Patrick J.; Nance, Stacy M.; Niland, Erin E.; Parsley, Megan E.; Ferguson, Meagan E.; Jiang, Guanglong; Ammakkanavar, Natraj R.; Einhorn, Lawrence H.; Cheng, Liang; Nassiri, Mehdi; Davidson, Darrell D.; Rushing, Daniel A.; Loehrer, Patrick J.; Pili, Roberto; Hanna, Nasser; Callaghan, J. Thomas; Skaar, Todd C.; Helft, Paul R.; Shahda, Safi; O’Neil, Bert H.; Schneider, Bryan P.; Medicine, School of MedicinePatients and methods: Patients with metastatic solid tumors who had progressed on at least one line of standard of care therapy were referred to the Indiana University Health Precision Genomics Program. Tumor samples were submitted for DNA & RNA next-generation sequencing, fluorescence in situ hybridization, and immunohistochemistry for actionable targets. A multi-disciplinary tumor board reviewed all results. For each patient, the ratio of progression-free survival (PFS) of the genomically guided line of therapy divided by the PFS of their prior line was calculated. Patients whose PFS ratio was ≥ 1.3 were deemed to have a meaningful improvement in PFS. Results: From April 2014-October 2015, 168 patients were evaluated and 101 patients achieved adequate clinical follow-up for analysis. 19 of 44 (43.2%) patients treated with genomically guided therapy attained a PFS ratio ≥ 1.3 vs. 3 of 57 (5.3%) treated with non-genomically guided therapy (p < 0.0001). Similarly, overall PFS ratios (irrespective of cutoff) were higher for patients with genomically guided therapy vs non-genomically guided therapy (p = 0.05). Further, patients treated with genomically guided therapy had a superior median PFS compared to those treated with non-genomically guided therapy (86 days vs. 49 days, p = 0.005, H.R. = 0.55, 95% C.I.:0.37-0.84). Conclusion: Patients with refractory metastatic cancer who receive genomically guided therapy have improved PFS ratios and longer median PFS compared to patients who do not receive genomically guided therapy.Item The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges(Frontiers, 2016-07-25) Landis, Benjamin J.; Ware, Stephanie M.; Department of Pediatrics, IU School of MedicineHuman cardiovascular malformations (CVMs) frequently have a genetic contribution. Through the application of novel technologies, such as next-generation sequencing, DNA sequence variants associated with CVMs are being identified at a rapid pace. While clinicians are now able to offer testing with NGS gene panels or whole exome sequencing to any patient with a CVM, the interpretation of genetic variation remains problematic. Variable phenotypic expression, reduced penetrance, inconsistent phenotyping methods, and the lack of high-throughput functional testing of variants contribute to these challenges. This article elaborates critical issues that impact the decision to broadly implement clinical molecular genetic testing in CVMs. Major benefits of testing include establishing a genetic diagnosis, facilitating cost-effective screening of family members who may have subclinical disease, predicting recurrence risk in offsprings, enabling early diagnosis and anticipatory management of CV and non-CV disease phenotypes, predicting long-term outcomes, and facilitating the development of novel therapies aimed at disease improvement or prevention. Limitations include financial cost, psychosocial cost, and ambiguity of interpretation of results. Multiplex families and patients with syndromic features are two groups where disease causation could potentially be firmly established. However, these account for the minority of the overall CVM population, and there is increasing recognition that genotypes previously associated with syndromes also exist in patients who lack non-CV findings. In all circumstances, ongoing dialog between cardiologists and clinical geneticists will be needed to accurately interpret genetic testing and improve these patients' health. This may be most effectively implemented by the creation and support of CV genetics services at centers committed to pursuing testing for patients.Item Emerging Role of Clinical Genetics in CKD(Elsevier, 2022-02-11) Devarajan, Prasad; Chertow, Glenn M.; Susztak, Katalin; Levin, Adeera; Agarwal, Rajiv; Stenvinkel, Peter; Chapman, Arlene B.; Warady, Bradley A.; Medicine, School of MedicineChronic kidney disease (CKD) afflicts 15% of adults in the United States, of whom 25% have a family history. Genetic testing is supportive in identifying and possibly confirming diagnoses of CKD, thereby guiding care. Advances in the clinical genetic evaluation include next-generation sequencing with targeted gene panels, whole exome sequencing, and whole genome sequencing. These platforms provide DNA sequence reads with excellent coverage throughout the genome and have identified novel genetic causes of CKD. New pathologic genetic variants identified in previously unrecognized biological pathways have elucidated disease mechanisms underlying CKD etiologies, potentially establishing prognosis and guiding treatment selection. Molecular diagnoses using genetic sequencing can detect rare, potentially treatable mutations, avoid misdiagnoses, guide selection of optimal therapy, and decrease the risk of unnecessary and potentially harmful interventions. Genetic testing has been widely adopted in pediatric nephrology; however, it is less frequently used to date in adult nephrology. Extension of clinical genetic approaches to adult patients may achieve similar benefits in diagnostic refinement and treatment selection. This review aimed to identify clinical CKD phenotypes that may benefit the most from genetic testing, outline the commonly available platforms, and provide examples of successful deployment of these approaches in CKD.Item Epigenetic Analysis of SV40 Minichromosomes(Wiley, 2017-08-11) Balakrishnan, Lata; Milavetz, Barry; Biology, School of ScienceSimian virus 40 (SV40) is one of the best-characterized members of the polyomavirus family of small DNA tumor viruses. It has a small genome of 5243 bp and utilizes cellular proteins for its molecular biology, with the exception of the T-antigen protein, which is coded by the virus and is involved in regulating transcription and directing replication. Importantly, SV40 exists as chromatin in both the virus particle and intracellular minichromosomes. These facts, combined with high yields of virus and minichromosomes following infection and ease of manipulation, have made SV40 an extremely useful model to study all aspects of eukaryotic molecular biology. This unit describes procedures for working with SV40 and preparing SV40 chromatin from infected cells and virus particles, as well as procedures for using SV40 chromatin to study epigenetic regulation.Item Estimating breast tissue-specific DNA methylation age using next-generation sequencing data(Springer, 2020-03-12) Castle, James R.; Lin, Nan; Liu, Jinpeng; Storniolo, Anna Maria V.; Shendre, Aditi; Hou, Lifang; Horvath, Steve; Liu, Yunlong; Wang, Chi; He, Chunyan; Medical and Molecular Genetics, School of MedicineBackground DNA methylation (DNAm) age has been widely accepted as an epigenetic biomarker for biological aging. Emerging evidence suggests that DNAm age can be tissue-specific and female breast tissue ages faster than other parts of the body. The Horvath clock, which estimates DNAm age across multiple tissues, has been shown to be poorly calibrated in breast issue. We aim to develop a model to estimate breast tissue-specific DNAm age. Methods Genome-wide DNA methylation sequencing data were generated for 459 normal, 107 tumor, and 45 paired adjacent-normal breast tissue samples. We determined a novel set of 286 breast tissue-specific clock CpGs using penalized linear regression and developed a model to estimate breast tissue-specific DNAm age. The model was applied to estimate breast tissue-specific DNAm age in different breast tissue types and in tumors with distinct clinical characteristics to investigate cancer-related aging effects. Results Our estimated breast tissue-specific DNAm age was highly correlated with chronological age (r = 0.88; p = 2.9 × 10−31) in normal breast tissue. Breast tumor tissue samples exhibited a positive epigenetic age acceleration, where DNAm age was on average 7 years older than respective chronological age (p = 1.8 × 10−8). In age-matched analyses, tumor breast tissue appeared 12 and 13 years older in DNAm age than adjacent-normal and normal breast tissue (p = 4.0 × 10−6 and 1.0 × 10−6, respectively). Both HER2+ and hormone-receptor positive subtypes demonstrated significant acceleration in DNAm ages (p = 0.04 and 3.8 × 10−6, respectively), while no apparent DNAm age acceleration was observed for triple-negative breast tumors. We observed a non-linear pattern of epigenetic age acceleration with breast tumor grade. In addition, early-staged tumors showed a positive epigenetic age acceleration (p = 0.003) while late-staged tumors exhibited a non-significant negative epigenetic age acceleration (p = 0.10). Conclusions The intended applications for this model are wide-spread and have been shown to provide biologically meaningful results for cancer-related aging effects in breast tumor tissue. Future studies are warranted to explore whether breast tissue-specific epigenetic age acceleration is predictive of breast cancer development, treatment response, and survival as well as the clinical utility of whether this model can be extended to blood samples.Item Genetic Alterations in Invasive Breast Carcinoma with a Glycogen-Rich Clear Cell Pattern: A Case Report(Karger, 2021-03-22) De la Sancha, Carlo; Ruiz-Cordero, Roberto; Popnikolov, Nikolay; Pathology and Laboratory Medicine, School of MedicineInvasive carcinoma with a glycogen-rich clear cell pattern (IC-GRCCP) is a rare and understudied subtype of invasive breast carcinoma of no special type (IBC-NST). Here we report the molecular characteristics of a mammary IC-GRCCP diagnosed in a 69-year-old woman. Next-generation sequencing of the tumor revealed an inv(1)(p36.12,q32.1) leading to loss-of-function of ARID1A gene, a MAP2K4 truncating mutation (p.E376), MYC amplification, a variant of uncertain significance of PTPRB gene (p.D1848N) and deep deletions of NCKAP5, CCNT2, MAP3K19, LRP1B, and KMT2A. The analysis of the involved pathways shows close resemblance to the ovarian clear cell carcinoma and indicates similarities in the molecular mechanisms of development of glycogen-rich clear cell carcinomas in different organs. Our findings and the literature review suggest new potential strategies for treatment of mammary IC-GRCCP, including epigenetic therapies, checkpoint inhibitors, radiation, or other double-strand DNA breaks-inducing agents. Nevertheless, larger studies are needed to substantiate those ideas.Item Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray(Taylor & Francis, 2021) Lin, Nan; Liu, Jinpeng; Castle, James; Wan, Jun; Shendre, Aditi; Liu, Yunlong; Wang, Chi; He, Chunyan; Medical and Molecular Genetics, School of MedicineA newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there was high concordance in methylation levels between the two platforms (Pearson correlation r = 0.98, P < 0.0001). However, we observed that TruSeq EPIC measurements provided a wider dynamic range and likely a higher quantitative sensitivity for CpGs that were either hypo- or hyper-methylated (β close to 0 or 1, respectively). In addition, when comparing different breast tissue types TruSeq EPIC identified more differentially methylated CpGs than EPIC-array, not only out of additional sites interrogated by TruSeq EPIC alone, but also out of common sites interrogated by both platforms. Our results suggest that both platforms show high reproducibility and reliability in genome-wide DNA methylation profiling, while TruSeq EPIC had a significant improvement over EPIC-array regarding genomic resolution and coverage. The wider dynamic range and likely higher precision of the estimates by the TruSeq EPIC may lead to the identification of novel differentially methylated markers that are associated with disease risk.Item High Diagnostic Yield and Clinical Utility of Next-Generation Sequencing in Children with Epilepsy and Neurodevelopmental Delays: A Retrospective Study(MDPI, 2024-09-06) Charouf, Daniel; Miller, Derryl; Haddad, Laith; White, Fletcher A.; Boustany, Rose-Mary; Obeid, Makram; Neurology, School of MedicineAdvances in genetics led to the identification of hundreds of epilepsy-related genes, some of which are treatable with etiology-specific interventions. However, the diagnostic yield of next-generation sequencing (NGS) in unexplained epilepsy is highly variable (10–50%). We sought to determine the diagnostic yield and clinical utility of NGS in children with unexplained epilepsy that is accompanied by neurodevelopmental delays and/or is medically intractable. A 5-year retrospective review was conducted at the American University of Beirut Medical Center to identify children who underwent whole exome sequencing (WES) or whole genome sequencing (WGS). Data on patient demographics, neurodevelopment, seizures, and treatments were collected. Forty-nine children underwent NGS with an overall diagnostic rate of 68.9% (27/38 for WES, and 4/7 for WGS). Most children (42) had neurodevelopmental delays with (18) or without (24) refractory epilepsy, and only three had refractory epilepsy without delays. The diagnostic yield was 77.8% in consanguineous families (18), and 61.5% in non-consanguineous families (26); consanguinity information was not available for one family. Genetic test results led to anti-seizure medication optimization or dietary therapies in six children, with subsequent improvements in seizure control and neurodevelopmental trajectories. Not only is the diagnostic rate of NGS high in children with unexplained epilepsy and neurodevelopmental delays, but also genetic testing in this population may often lead to potentially life-altering interventions.Item The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics(Springer BioMed Central, 2019-12-30) Mathé, Ewy; Zhang, Chi; Wang, Kai; Ning, Xia; Guo, Yan; Zhao, Zhongming; Medical and Molecular Genetics, School of MedicineThe goal of this editorial is to summarize the 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) conference that took place on June 9–11, 2019 in The Ohio State University, Columbus, OH, and to provide an introductory summary of the seven articles presented in this supplement issue. ICIBM 2019 hosted four keynote speakers, four eminent scholar speakers, five tutorials and workshops, twelve concurrent sessions and a poster session, totaling 23 posters, spanning state-of-the-art developments in bioinformatics, genomics, next-generation sequencing (NGS) analysis, scientific databases, cancer and medical genomics, and computational drug discovery. A total of 105 original manuscripts were submitted to ICIBM 2019, and after careful review, seven were selected for this supplement issue. These articles cover methods and applications for functional annotations of miRNA targeting, clonal evolution of bacterial cells, gene co-expression networks that describe a given phenotype, functional binding site analysis of RNA-binding proteins, normalization of genome architecture mapping data, sample predictions based on multiple NGS data types, and prediction of an individual’s genetic admixture given exonic single nucleotide polymorphisms data.