Utility Of Genome Sequencing Research Articles

Genome Sequencing Enhances the Diagnostic Yield and Expands the Genetic Landscape of Male Breast Cancer

PurposeTo understand the broader genetic landscape of Male Breast Cancer (MBC), focusing on the utility of genome sequencing (GS) beyond BRCA1/2 (HGNC: 1100, 1101) variants. Methods24 MBC patients underwent a multi-step genetic analysis. Initial screening targeted BRCA1/2 variants followed by GS to identify pathogenic/likely pathogenic (P/LP) germline variants through a three-tiered classification. Polygenic risk score (PRS) analysis was further incorporated using a model for female breast cancer with 2666 non-cancer controls. Exome sequencing (ES) was employed to transition from germline to somatic investigations, assessing second-hit variant and mutational signatures. ResultsThe GS analysis unveiled previously unrecognized P/LP germline variants in BARD1, ATR, BRIP1, and CHEK2 (HGNC: 952, 882, 20473, 16627) among 21 BRCA1/2-negative MBC patients, elevating the diagnostic yield from 12.5% to 33.0% in all MBC. Elevated average PRS was noted compared to controls, with a significant correlation to early-onset MBC when combined with high-penetrance germline pathogenic variants (P = 1.10×10-4). ES analysis further identified significant somatic oncogenic drivers and revealed a dominant mutational signature SBS3 across BRCA1/2-negative samples, reinforcing the contribution of HRD underlying the MBC development. ConclusionOur findings extended the MBC genetic spectrum beyond BRCA1/2 and highlighted the intricate interplay of monogenic and polygenic predispositions, presenting a comprehensive MBC genomic profile.

Utility of Genome Sequencing After Nondiagnostic Exome Sequencing in Unexplained Pediatric Epilepsy.

Epilepsy is the most common neurological disorder of childhood. Identifying genetic diagnoses underlying epilepsy is critical to developing effective therapies and improving outcomes. Most children with non-acquired (unexplained) epilepsy remain genetically unsolved, and the utility of genome sequencing after nondiagnostic exome sequencing is unknown. To determine the diagnostic (primary) and clinical (secondary) utility of genome sequencing after nondiagnostic exome sequencing in individuals with unexplained pediatric epilepsy. This cohort study performed genome sequencing and comprehensive analyses for 125 participants and available biological parents enrolled from August 2018 to May 2023, with data analysis through April 2024 and clinical return of diagnostic and likely diagnostic genetic findings. Clinical utility was evaluated. Pediatric referral center. Participants with unexplained pediatric epilepsy and previous nondiagnostic exome sequencing; biological parents when available. Short-read genome sequencing and analysis. Primary outcome measures were the diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding, and the unique diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding that required genome sequencing. The secondary outcome measure was clinical utility of genome sequencing, defined as impact on evaluation, treatment, or prognosis for the participant or their family. 125 participants (58 [46%] female) were enrolled with median age at seizure onset 3 [IQR 1.25, 8] years, including 44 (35%) with developmental and epileptic encephalopathies. The diagnostic yield of genome sequencing was 7.2% (9/125), with diagnostic genetic findings in five cases and likely diagnostic genetic findings in four cases. Among the solved cases, 7/9 (78%) required genome sequencing for variant detection (small copy number variant, three noncoding variants, and three difficult to sequence small coding variants), for a unique diagnostic yield of genome sequencing of 5.6% (7/125). Clinical utility was documented for 4/9 solved cases (44%). These findings suggest that genome sequencing can have diagnostic and clinical utility after nondiagnostic exome sequencing and should be considered for patients with unexplained pediatric epilepsy.

Utility of genome sequencing in exome-negative pediatric patients with neurodevelopmental phenotypes.

Exome sequencing (ES) has emerged as an essential tool in the evaluation of neurodevelopmental disorders (NDD) of unknown etiology. Genome sequencing (GS) offers advantages over ES due to improved detection of structural, copy number, repeat number and non-coding variants. However, GS is less commonly utilized due to higher cost and more intense analysis. Here, we present nine cases of pediatric NDD that were molecularly diagnosed with GS between 2017 and 2022, following non-diagnostic ES. All individuals presented with global developmental delay or regression. Other features present in our cohort included epilepsy, white matter abnormalities, brain malformation and dysmorphic features. Two cases were diagnosed on GS due to newly described gene-disease relationship or variant reclassification (MAPK8IP3, CHD3). Additional features missed on ES that were later detected on GS were: intermediate-size deletions in three cases who underwent ES that were not validated for CNV detection, pathogenic variants within the non-protein coding genes SNORD118 and RNU7-1, pathogenic variant within the promoter region of GJB1, and a coding pathogenic variant within BCAP31 which was not sufficiently covered on ES. GS following non-diagnostic ES led to the identification of pathogenic variants in this cohort of nine cases, four of which would not have been identified by reanalysis alone.

Exploring the impact and utility of genomic sequencing in established CKD.

Clinical genetics is increasingly recognized as an important area within nephrology care. Clinicians require awareness of genetic kidney disease to recognize clinical phenotypes, consider use of genomics to aid diagnosis, and inform treatment decisions. Understanding the broad spectrum of clinical phenotypes and principles of genomic sequencing is becoming increasingly required in clinical nephrology, with nephrologists requiring education and support to achieve meaningful patient outcomes. Establishment of effective clinical resources, multi-disciplinary teams and education is important to increase application of genomics in clinical care, for the benefit of patients and their families. Novel applications of genomics in chronic kidney disease include pharmacogenomics and clinical translation of polygenic risk scores. This review explores established and emerging impacts and utility of genomics in kidney disease.

Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms.

Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.

Parents' Perspectives on the Utility of Genomic Sequencing in the Neonatal Intensive Care Unit.

It is critical to understand the wide-ranging clinical and non-clinical effects of genome sequencing (GS) for parents in the NICU context. We assessed parents' experiences with GS as a first-line diagnostic tool for infants with suspected genetic conditions in the NICU. Parents of newborns (N = 62) suspected of having a genetic condition were recruited across five hospitals in the southeast United States as part of the SouthSeq study. Semi-structured interviews (N = 78) were conducted after parents received their child's sequencing result (positive, negative, or variants of unknown significance). Thematic analysis was performed on all interviews. Key themes included that (1) GS in infancy is important for reproductive decision making, preparing for the child's future care, ending the diagnostic odyssey, and sharing results with care providers; (2) the timing of disclosure was acceptable for most parents, although many reported the NICU environment was overwhelming; and (3) parents deny that receiving GS results during infancy exacerbated parent-infant bonding, and reported variable impact on their feelings of guilt. Parents reported that GS during the neonatal period was useful because it provided a "backbone" for their child's care. Parents did not consistently endorse negative impacts like interference with parent-infant bonding.

EP400: Utility of genome sequencing in CNV identification in an immune disorders cohort

Chromosomal microarray (CMA) enables the detection of copy number changes within exon or gene-level resolution depending on probe density and gene coverage. Genome sequencing (GS) can circumvent these resolution issues through detection of smaller copy number changes enabled by uniformity of coverage that is not possible by exome sequencing (ES). Copy number variants (CNVs) can add to the diagnostic yield of inborn errors of immunity (IEI); however, the role of genome sequencing in identifying CNVs in IEI is not well understood.

Clinical utility of genome sequencing using liquid biopsy assay in the treatment of pancreatic cancer

Clinical utility of genome sequencing using liquid biopsy assay in the treatment of pancreatic cancer

Overview of genomic surveillance related to Severe Acute Respiratory Syndrom Coronavirus 2 (SARS- CoV-2)

Since the start of the Severe Acute Respiratory Syndrom Coronavirus 2 (SARS-CoV-2) pandemic, several thousand of variants circulated and others are emerging. Therefore, genomic surveillance is crucial, which aims to detect the emergence of new variants, in particular Variants of Concern (VOC) and to assess the impact of priority mutations on the transmissibility and lethality of the virus, the performance of viral diagnostic methods and vaccine efficiency. An overview of available papers was performed to understand conduct, tools and utility of genomic sequencing and surveillance related to Covid-19 disease. We also report the experience of Morocco in this filed through available data. A national SARS-Cov-2 genomic consortium has been established in order to continuously inform the health authorities of the genetic evolution of circulating strains in Morocco. Genomic sequencing shows that Moroccan genomes spread did not show a predominant SARS-CoV-2 lineage. Genomes are dispersed across the evolutionary tree of SARS-CoV-2 and held between 4 and 16 mutations. As the pandemic ongoing, continuous genomic surveillance and regular sequencing are fundamental to understand the spread of SARS-CoV-2, to rapidly identify potential global transmission networks and to consolidate response strategies especially targeted Covid-19 vaccination.

Abstract P6-08-23: Disclosure of familial implications of pathogenic BRCA1/2 to probands: Opportunity for prompting family communication

Abstract Familial communication of pathogenic BRCA1/2 results is necessary to maximize the clinical utility of genomic sequencing and its public health benefits. Cascade BRCA1/2 genetic testing is suboptimal and practical strategies for promoting familial testing are needed. Disclosure of BRCA1/2 results present opportunities to counsel probands about familial communication. Little is known about what familial communication recommendations are offered to probands by genetic counselors (GCs). We examined differences in how GCs discussed familial implications of pathogenic BRCA1/2 results based on: specificity of familial risk-messaging; offer of logistical help for relatives; and, provision of family letters. We completed structured content analysis of 343 BRCA1/2 result disclosure notes abstracted from electronic medical records (EMRs), for probands seen at MD Anderson Cancer Center from 2014-2019. Probands were 90.7% female, median age of 49 years, 44.3% non-White, and were counseled by 22 unique GCs with mean post-graduate experience of 4.2 years. 51.0% of notes described specific at-risk relatives who would benefit from genetic counseling; the remainder described familial implications more generically. The practice of including specific information differed widely among individual GCs. 29.1% provided information on logistical genetic counseling assistance for relatives (e.g., targeted testing cost, assistance locating GCs or testing services for underinsured). In particular, assistance locating GCs internationally through institutional databases or through GCs’ professional networks were particularly appreciated by patients. More experienced GCs were more likely to provide detailed familial implication information (p=<0.001) and offer logistical help (p=0.002). Presence of an accompanying relative to an in-person appointment (n=78) did not change the specificity of familial implications offered, compared to unaccompanied (n=95) or telephone disclosures (n=165) (p=0.78). The provision of family letters was mentioned in 47.2% of notes, but the intended recipient or purpose were frequently not specified. When specified, some GCs actively encouraged patients to distribute family letters to relatives while others only mentioned that letters would be mailed to patients. 58 of 343 patients had one or more accompanying VUS in addition to pathogenic BRCA1/2 mutation. In 67% of VUS cases, VUS implications were discussed in detail, including non-indication for familial testing. Some notes indicated familial communication primarily as a means to determine paternal/maternal inheritance of mutation with little to no emphasis on the benefits of cascade testing. While determining inheritance patterns of BRCA1/2 is important for targeted testing of at-risk relatives, counseling can be framed as altruistic opportunities to benefit relatives through cascade genetic testing which may be a more persuasive strategy to promote familial communication. Pathogenic BRCA1/2 disclosure appointments were noted as overwhelming experiences for some patients. In such cases, GCs may prioritize information that impacts patients’ immediate care over familial information to reduce information overload. Although there may be discordance between EMR disclosure notes and actual counseling, findings suggest that offering specific risk-messaging, logistical help and explaining intended recipients of family letters are opportunities for improving familial communication. The heterogeneity in disclosure notes between GCs may reflect their differing philosophies of the utility of writing detailed versus specific notes. Additional investigation of GC perspectives and motivations for writing disclosure notes of varying styles and its impact on familial communication is warranted. Citation Format: Sukh Makhnoon, Banu Arun, Robert J Volk, Susan K Peterson. Disclosure of familial implications of pathogenic BRCA1/2 to probands: Opportunity for prompting family communication [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-23.

Cancer patients’ views and understanding of genome sequencing: a qualitative study

BackgroundLittle is known about knowledge of, and attitudes towards, genome sequencing (GS) among individuals with a personal history of cancer who decide to undergo GS. This qualitative study aimed to...

Primary care provider perspectives on using genomic sequencing in the care of healthy children.

Genome sequencing (GS) studies involving healthy children can advance scientific knowledge of genetic variation. Little research has examined primary care providers' views on using GS in this context. This study explored primary care provider perspectives on the use of GS in research and the care of healthy children. We conducted semi-structured interviews with 16 providers discussing their views on GS research and receiving results. Interviews were analyzed by thematic analysis and constant comparison. Participants were family physicians (11/16) and primary care pediatricians (5/16) in practice for >10 years (11/16). Participants valued GS in healthy children for research purposes; however, opinions diverged on using the results in primary care. Proponents valued using results for surveillance and prevention in healthy children. Skeptics questioned the clinical utility of results and the appropriateness of applying research data in primary care. Both groups shared concerns over opportunistic screening, validity, and interpretation of results, increased health system costs and inequities, and genetic discrimination. Primary care providers were ambivalent about the appropriateness and utility of GS in the care of healthy children. Providers feel unprepared and unsure of their obligations in disclosing these results. Providers do not feel they are equipped with the necessary resources and training to support their patients in using GS results in their care.

Delivering genome sequencing in clinical practice: an interview study with healthcare professionals involved in the 100 000 Genomes Project

ObjectivesGenome sequencing is poised to be incorporated into clinical care for diagnoses of rare diseases and some cancers in many parts of the world. Healthcare professionals are key stakeholders in...

Abstract IA02: Defects in DNA repair genes revealed by clinical sequencing of advanced cancer patients

Abstract In 2011, we introduced the Mi-Oncoseq program, an IRB-approved protocol to carry out integrative sequencing of advanced cancer patients. It was one of the first comprehensive DNA and RNA sequencing programs offered for cancer patients. The purpose of this program was to determine the utility of genomic sequencing of tumors and germline coupled with a multi-disciplinary Precision Medicine Tumor Board (PMTB) in the management of advanced cancer patients. Collectively across all patient cohorts we have enrolled over 1500 patients since inception of Mi-Oncoseq where molecular results for both somatic and germline aberrations are returned to physicians. Both common and rare mutations were identified in numerous cellular pathways that are involved in carcinogenesis including those in the DNA repair pathway. We identified homozygous deletions, deleterious mutations and/or LOH in genes including BRCA1/2, ATM, Fanconi's anemia genes, and CHEK2 that are potentially actionable. For example, a multi-institutional, collaborative SU2C-PCF study of men with metastatic castrate-resistant prostate cancer (mCRPC) found that treatment with the PARP inhibitor olaparib in patients whose prostate cancers were no longer responding to standard treatments and who had defects in DNA-repair genes led to a high response rate (Mateo et al. NEJM, 2015). Additionally, a follow-up study found 11.8% of mCRPC patients had a germline mutation in a DNA-repair gene, including moderate risk genes (ATM, CHEK2, PALB2, RAD51D) for which clinical testing criteria do not exist (Pritchard et al, NEJM, 2016). Most of these patients would not qualify for germline genetic testing under current clinical care models. Our studies demonstrate that DNA repair mutations are common in mCRPC patients who may benefit from therapies such as PARP inhibitors and when identified in the germline, could have a significant impact on their family members where early cancer screening could be implemented as appropriate. Citation Format: Arul Chinnaiyan. Defects in DNA repair genes revealed by clinical sequencing of advanced cancer patients [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr IA02.

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the ‘distance to resistance’. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings.

Abstract PR01: Precision in Pediatric Sequencing (PIPseq): Clinical implementation of genomic sequencing into pediatric hematology-oncology practice

Abstract Background: Molecular characterization of tumor and/or host has the potential to advance the management of pediatric cancer and high risk hematologic disease, but the clinical utility of integrating genomic profiling into standard clinical practice has been limited. The PIPseq Program at Columbia University has instituted prospective CLIA-compliant genomic sequencing for newly diagnosed, high risk, relapsed or refractory pediatric cancer patients and patients referred for bone marrow transplantation. Methods: Families are consented for clinical cancer whole-exome sequencing (cWES) or constitutional whole-exome sequencing (WES) with opt out options for return of results, exclusion of results from medical records, receipt of American College of Medical Genetics (ACMG) recommended secondary germline variants, and data/ sample use in research. Molecular characterization utilizes next generation cWES, WES, RNAseq (transcriptome), or targeted sequencing of select cancer genes. Clinical cancer reports include: known tumor type-specific actionable somatic mutations (Tier 1); somatic mutations actionable in other tumor types, in targetable pathways, or in well-established cancer genes (Tier 2); other somatic mutations in cancer genes (Tier 3); and somatic variants of uncertain significance (VUS; Tier 4). Reports for cWES testing also note translocations, significantly over expressed genes, segmental copy number variation, and germline variants. Institutional Review Board approval was obtained to conduct a retrospective review of results to date. Five categories were developed to assess clinical utility and describe significance: 1) diagnostic, 2) prognostic, 3) potentially actionable target, 4) other critical role in decision making, and 5) implications for health maintenance and genetic counseling. Results: Since January 2014, adequate tissue samples were available for 47 patients, including 31 (66%) with solid tumors and 16 (34%) with hematologic conditions. Testing included cWES (n=8), cWES with transcriptome (n=15), transcriptome only (n=1), targeted somatic panel (n=8), constitutional WES only (n=6), and multiple sequencing platforms (n=7). Normal tissue was obtained from buccal swab (n=8), blood (n=18), and unaffected tissue (n=1). Three families opted out of receiving secondary findings. Genomic aberrations were reported in 41/47 patients. Of the 127 cancer alterations found, 70 (55%) were in 15 patients with hematologic disease (median 2, range 1-11) and 57 (45%), were in 26 patients with solid tumors (median 1, range 1-6). Among the hematologic cases, alterations of known or potential clinical relevance were categorized as Tier 1 (n=0), Tier 2 (n=27), Tier 3 (n=2) mutation, or translocation (n=4); whereas in solid tumors these were categorized as Tier 1 (n=1), Tier 2 (n=14), Tier 3 (n=3) mutation, or translocation (n=9). Twenty-four Tier 4 somatic VUS were identified in hematologic specimens and 26 in solid tumor specimens. Genomic interrogation informed diagnosis in 10 patients (3 previously unknown); provided new prognostic information in 4; identified potentially actionable targets in 15; influenced clinical decision making regarding bone marrow transplant in 2; and revealed cancer or other disease predisposition in 7. Secondary germline ACMG findings in BRCA1 and PMS2 were found. Germline APC mutation was confirmed in one patient and germline VUS in SDHC was seen in another. Novel germline findings were also observed in RUNX1, MLL2 and DICER1. Overall, the PIPseq platform provided clinically impactful results in 30/47 cases (64%). Conclusions: Utilizing a CLIA-compliant prospective WES-based platform, more than half of selected patients derived clinically impactful information. The potential clinical utility of genomic sequencing in pediatric hematology-oncology has likely been underestimated. This abstract is also presented as Poster 50. Citation Format: Julia L. Glade Bender, Jennifer A. Oberg, Maria Luisa Sulis, Filamon Dela Cruz, Anthony N. Sireci, Susan J. Hsiao, Darrell J. Yamashiro, Carrie Koval, Wendy K. Chung, Stephen G. Emerson, Rebecca Zylber, Samantha Cano, Danielle P. Denney, Stuart Andrews, Peter L. Nagy, Mahesh M. Mansukhani, Andrew L. Kung. Precision in Pediatric Sequencing (PIPseq): Clinical implementation of genomic sequencing into pediatric hematology-oncology practice. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr PR01.