Review of 200 consecutive patients with mutation profiling in a lung cancer individualized medicine clinic.

e19013 Background: Mutation profiling to assess for potentially druggable mutations in NSCLC is being offered at an increasing number of cancer centers throughout North America and internationally. Although data continue to accumulate for the potential value of mutation testing in designing chemotherapeutic regimens, the treatment impact of obtaining information beyond assessment of EGFR and ALK status remains unclear. How best to obtain and clinically utilize these data, including information from exome and whole genome sequencing, also remains unclear. Methods: Patients were reviewed electronically in a multidisciplinary conference regarding indications for testing and results of mutation profiling from various methods, including the mass-spec based LungCarta test, targeted NexGen sequencing, exome, and whole genome sequencing. Outcomes of the multidisciplinary review were communicated back to treating physicians. Results: Mutation testing was performed on 200 patients using a variety of approaches. The majority (>150) were surgically resected stage I and II tumors. Mutations in at least 1 major cancer driver gene, including EGFR, KRAS, MET, BRAF and PIK3CA, were found in 47% of all patients tested. EGFR mutations were present in 14.8% of patients tested, KRAS 21.3%, BRAF 2.6%, PIK3CA 3.2%, and MET 4.5%. A total of 8 patients underwent either exome or whole genome sequencing. A limited number of patients (<10) had mutation results that impacted treatment decisions from this cohort. Conclusions: Mutation profiling can influence treatment decisions in NSCLC, but at a low frequency. The role of exome and or whole genome sequencing for patients with NSCLC is evolving and remains undefined.

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A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families

Human Molecular Genetics ◽

10.1093/hmg/ddaa016 ◽

2020 ◽

Vol 29 (6) ◽

pp. 967-979 ◽

Cited By ~ 6

Author(s):

Revital Bronstein ◽

Elizabeth E Capowski ◽

Sudeep Mehrotra ◽

Alex D Jansen ◽

Daniel Navarro-Gomez ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Diagnosis ◽

Genetic Diagnostics ◽

Whole Genome ◽

Unique Challenge ◽

Coding Regions ◽

Pathogenic Variants ◽

Number Of Patients ◽

Coding Variants

Abstract Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.

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Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features

Nature Communications ◽

10.1038/s41467-020-20887-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Pauline A. J. Mendelaar ◽

Marcel Smid ◽

Job van Riet ◽

Lindsay Angus ◽

Mariette Labots ◽

...

Keyword(s):

Colorectal Cancer ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fragile Sites ◽

Response To Treatment ◽

Whole Genome Sequencing Data ◽

Driver Gene ◽

Whole Genome ◽

Sequencing Data ◽

Genomic Landscape

AbstractIn contrast to primary colorectal cancer (CRC) little is known about the genomic landscape of metastasized CRC. Here we present whole genome sequencing data of metastases of 429 CRC patients participating in the pan-cancer CPCT-02 study (NCT01855477). Unsupervised clustering using mutational signature patterns highlights three major patient groups characterized by signatures known from primary CRC, signatures associated with received prior treatments, and metastasis-specific signatures. Compared to primary CRC, we identify additional putative (non-coding) driver genes and increased frequencies in driver gene mutations. In addition, we identify specific genes preferentially affected by microsatellite instability. CRC-specific 1kb-10Mb deletions, enriched for common fragile sites, and LINC00672 mutations are associated with response to treatment in general, whereas FBXW7 mutations predict poor response specifically to EGFR-targeted treatment. In conclusion, the genomic landscape of mCRC shows defined changes compared to primary CRC, is affected by prior treatments and contains features with potential clinical relevance.

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Landscape of Driver Gene Events, Biomarkers and Druggable Targets Identified by Whole Genome Sequencing of Glioblastomas

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab177 ◽

2021 ◽

Author(s):

Wesley S van de Geer ◽

Youri Hoogstrate ◽

Kaspar Draaisma ◽

Pierre A Robe ◽

Sander Bins ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mutational Analysis ◽

Driver Gene ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Driver Genes ◽

Improve Patient Survival ◽

Age Related ◽

Druggable Targets

Abstract Background The survival of glioblastoma patients is poor. Median survival after diagnosis is 15 months, despite treatment involving surgical resection, radiotherapy and/or temozolomide chemotherapy. Identification of novel targets and stratification strategies of glioblastoma patients to improve patient survival is urgently needed. Whole genome sequencing (WGS) is the most comprehensive means to identify such DNA-level targets. We report a unique set of WGS samples along with comprehensive analyses of the glioblastoma genome and potential clinical impact of WGS. Methods Our cohort consisted of 42 glioblastoma tumor tissue and matched whole-blood samples, which were whole-genome sequenced as part of the CPCT-02 study. Somatic single-nucleotide variants, small insertions/deletions, multi-nucleotide variants, copy-number alterations (CNAs) and structural variants were analyzed. These aberrations were harnessed to investigate driver genes, enrichments in CNAs, mutational signatures, fusion genes and potential targeted therapies. Results Tumor mutational burden (TMB) was similar to other WGS efforts (1-342 mutations per megabase pair). Mutational analysis in low TMB samples showed that the age-related CpG demethylation signature was dominant, while hyper- and ultramutated tumors had additional defective DNA mismatch repair signatures and showed microsatellite instability in their genomes. We detected chromothripsis in 24% of our cohort, recurrently on chromosomes 1 and 12. Recurrent non-coding regions only resulted in TERT promoter variants. Finally, we found biomarkers and potentially druggable changes in all but one of our tumor samples. Conclusions With high quality WGS data and comprehensive methods, we identified the landscape of driver gene events and druggable targets in glioblastoma patients.

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A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families

10.1101/766717 ◽

2019 ◽

Author(s):

Revital Bronstein ◽

Elizabeth E. Capowski ◽

Sudeep Mehrotra ◽

Alex D. Jansen ◽

Daniel Navarro-Gomez ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Diagnosis ◽

Genetic Diagnostics ◽

Whole Genome ◽

Unique Challenge ◽

Coding Regions ◽

Pathogenic Variants ◽

Number Of Patients ◽

Coding Variants

AbstractInherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient induced pluripotent stem cell (iPSC) derived retinal organoids (ROs) transcriptome analysis. With this approach we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.

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Abstract 25: Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions

10.1158/1557-3265.pmsclingen15-25 ◽

2016 ◽

Author(s):

Stephen Benz ◽

J Zackary Sanborn ◽

Nicole S. Hensley ◽

Todd Hembrough ◽

Charles J. Vaske ◽

...

Keyword(s):

Cervical Cancer ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Quantitative Proteomics ◽

Treatment Decisions ◽

Clinical Treatment ◽

Her2 Overexpression ◽

Whole Genome ◽

Omics Analysis

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Study protocol: Whole genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE)

BMC Medical Genomics ◽

10.1186/s12920-020-00814-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Kris G. Samsom ◽

Linda J. W. Bosch ◽

Luuk J. Schipper ◽

Paul Roepman ◽

Ewart de Bruijn ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Molecular Diagnostics ◽

Clinical Decision Making ◽

Tissue Sample ◽

Clinical Care ◽

Precision Oncology ◽

Whole Genome ◽

Routine Clinical Care ◽

Number Of Patients

Abstract Background ‘Precision oncology’ can ensure the best suitable treatment at the right time by tailoring treatment towards individual patient and comprehensive tumour characteristics. In current molecular pathology, diagnostic tests which are part of the standard of care (SOC) only cover a limited part of the spectrum of genomic changes, and often are performed in an iterative way. This occurs at the expense of valuable patient time, available tissue sample, and interferes with ‘first time right’ treatment decisions. Whole Genome Sequencing (WGS) captures a near complete view of genomic characteristics of a tumour in a single test. Moreover, WGS facilitates faster implementation of new treatment relevant biomarkers. At present, WGS mainly has been applied in study settings, but its performance in a routine diagnostic setting remains to be evaluated. The WIDE study aims to investigate the feasibility and validity of WGS-based diagnostics in clinical practice. Methods 1200 consecutive patients in a single comprehensive cancer centre with (suspicion of) a metastasized solid tumour will be enrolled with the intention to analyse tumour tissue with WGS, in parallel to SOC diagnostics. Primary endpoints are (1) feasibility of implementation of WGS-based diagnostics into routine clinical care and (2) clinical validation of WGS by comparing identification of treatment-relevant variants between WGS and SOC molecular diagnostics. Secondary endpoints entail (1) added clinical value in terms of additional treatment options and (2) cost-effectiveness of WGS compared to SOC diagnostics through a Health Technology Assessment (HTA) analysis. Furthermore, the (3) perceived impact of WGS-based diagnostics on clinical decision making will be evaluated through questionnaires. The number of patients included in (experimental) therapies initiated based on SOC or WGS diagnostics will be reported with at least 3 months follow-up. The clinical efficacy is beyond the scope of WIDE. Key performance indicators will be evaluated after every 200 patients enrolled, and procedures optimized accordingly, to continuously improve the diagnostic performance of WGS in a routine clinical setting. Discussion WIDE will yield the optimal conditions under which WGS can be implemented in a routine molecular diagnostics setting and establish the position of WGS compared to SOC diagnostics in routine clinical care.

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Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients

Genome Medicine ◽

10.1186/s13073-021-00855-5 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Henrik Stranneheim ◽

Kristina Lagerstedt-Robinson ◽

Måns Magnusson ◽

Malin Kvarnung ◽

Daniel Nilsson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rare Diseases ◽

De Novo ◽

Genomic Medicine ◽

Uniparental Disomy ◽

Healthcare Setting ◽

University Hospital ◽

Whole Genome ◽

Number Of Patients

Abstract Background We report the findings from 4437 individuals (3219 patients and 1218 relatives) who have been analyzed by whole genome sequencing (WGS) at the Genomic Medicine Center Karolinska-Rare Diseases (GMCK-RD) since mid-2015. GMCK-RD represents a long-term collaborative initiative between Karolinska University Hospital and Science for Life Laboratory to establish advanced, genomics-based diagnostics in the Stockholm healthcare setting. Methods Our analysis covers detection and interpretation of SNVs, INDELs, uniparental disomy, CNVs, balanced structural variants, and short tandem repeat expansions. Visualization of results for clinical interpretation is carried out in Scout—a custom-developed decision support system. Results from both singleton (84%) and trio/family (16%) analyses are reported. Variant interpretation is done by 15 expert teams at the hospital involving staff from three clinics. For patients with complex phenotypes, data is shared between the teams. Results Overall, 40% of the patients received a molecular diagnosis ranging from 19 to 54% for specific disease groups. There was heterogeneity regarding causative genes (n = 754) with some of the most common ones being COL2A1 (n = 12; skeletal dysplasia), SCN1A (n = 8; epilepsy), and TNFRSF13B (n = 4; inborn errors of immunity). Some causative variants were recurrent, including previously known founder mutations, some novel mutations, and recurrent de novo mutations. Overall, GMCK-RD has resulted in a large number of patients receiving specific molecular diagnoses. Furthermore, negative cases have been included in research studies that have resulted in the discovery of 17 published, novel disease-causing genes. To facilitate the discovery of new disease genes, GMCK-RD has joined international data sharing initiatives, including ClinVar, UDNI, Beacon, and MatchMaker Exchange. Conclusions Clinical WGS at GMCK-RD has provided molecular diagnoses to over 1200 individuals with a broad range of rare diseases. Consolidation and spread of this clinical-academic partnership will enable large-scale national collaboration.

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Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival

Nature Communications ◽

10.1038/s41467-021-21026-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jiwei Bai ◽

Jianxin Shi ◽

Chuzhong Li ◽

Shuai Wang ◽

Tongwu Zhang ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Skull Base ◽

Genome Sequencing ◽

Unknown Etiology ◽

High Recurrence Rate ◽

Driver Gene ◽

Whole Genome ◽

Genomic Alterations ◽

Skull Base Chordomas ◽

Skull Base Chordoma

AbstractChordoma is a rare bone tumor with an unknown etiology and high recurrence rate. Here we conduct whole genome sequencing of 80 skull-base chordomas and identify PBRM1, a SWI/SNF (SWItch/Sucrose Non-Fermentable) complex subunit gene, as a significantly mutated driver gene. Genomic alterations in PBRM1 (12.5%) and homozygous deletions of the CDKN2A/2B locus are the most prevalent events. The combination of PBRM1 alterations and the chromosome 22q deletion, which involves another SWI/SNF gene (SMARCB1), shows strong associations with poor chordoma-specific survival (Hazard ratio [HR] = 10.55, 95% confidence interval [CI] = 2.81-39.64, p = 0.001) and recurrence-free survival (HR = 4.30, 95% CI = 2.34-7.91, p = 2.77 × 10−6). Despite the low mutation rate, extensive somatic copy number alterations frequently occur, most of which are clonal and showed highly concordant profiles between paired primary and recurrence/metastasis samples, indicating their importance in chordoma initiation. In this work, our findings provide important biological and clinical insights into skull-base chordoma.

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