scholarly journals Clinical Pan-Cancer Assessment of Mismatch Repair Deficiency Using Tumor-Only, Targeted Next-Generation Sequencing

2020 ◽  
pp. 1084-1097
Author(s):  
Adem Albayrak ◽  
Ana C. Garrido-Castro ◽  
Marios Giannakis ◽  
Renato Umeton ◽  
Monica Devi Manam ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mismatch Repair ◽  
Checkpoint Inhibitors ◽  
Cost Effective ◽  
Tumor Type ◽  
Next Generation ◽  
Clinical Value ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing ◽  
Screening Approaches

PURPOSE Given regulatory approval of immune checkpoint inhibitors in patients with mismatch repair–deficient (MMR-D) cancers agnostic to tumor type, it has become important to characterize occurrence of MMR-D and develop cost-effective screening approaches. Using a next-generation sequencing (NGS) panel (OncoPanel), we developed an algorithm to identify MMR-D frequency in tumor samples and applied it in a clinical setting with pathologist review. METHODS To predict MMR-D, we adapted methods described previously for use in NGS panels, which assess patterns of single base-pair insertion or deletion events occurring in homopolymer regions. Tumors assayed with OncoPanel between July 2013 and July 2018 were included. For tumors tested after June 2017, sequencing results were presented to pathologists in real time for clinical MMR determination, in the context of tumor mutation burden, other mutational signatures, and clinical data. RESULTS Of 20,301 tumors sequenced, 2.7% (553) were retrospectively classified as MMR-D by the algorithm. Of 4,404 samples with pathologist sign-out of MMR status, the algorithm classified 147 (3.3%) as MMR-D: in 116 cases, MMR-D was confirmed by a pathologist, five cases were overruled by the pathologist, and 26 were assessed as indeterminate. Overall, the highest frequencies of OncoPanel-inferred MMR-D were in endometrial (21%; 152/723), colorectal (9.7%; 169/1,744), and small bowel (9.3%; 9/97) cancers. When algorithm predictions were compared with historical MMR immunohistochemistry or polymerase chain reaction results in a set of 325 tumors sequenced before initiation of pathologist assessment, the overall sensitivity and specificity of the algorithm were 91.1% and 98.2%, respectively. CONCLUSION We show that targeted, tumor-only NGS can be leveraged to determine MMR signatures across tumor types, suggesting that broader biomarker screening approaches may have clinical value.

Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing

2011 ◽  
Vol 6 (12) ◽  
pp. 1870-1886 ◽  
Author(s):  
Magdalena Harakalova ◽  
Michal Mokry ◽  
Barbara Hrdlickova ◽  
Ivo Renkens ◽  
Karen Duran ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cost Effective ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

scholarly journals Targeted next‐generation sequencing of 22 mismatch repair genes identifies Lynch syndrome families

2016 ◽  
Vol 5 (5) ◽  
pp. 929-941 ◽  
Author(s):  
Bente A. Talseth‐Palmer ◽  
Denis C. Bauer ◽  
Wenche Sjursen ◽  
Tiffany J. Evans ◽  
Mary McPhillips ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lynch Syndrome ◽  
Mismatch Repair ◽  
Mismatch Repair Genes ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Repair Genes ◽  
Generation Sequencing

scholarly journals Validation of a targeted next-generation sequencing approach to detect mismatch repair deficiency in colorectal adenocarcinoma

2018 ◽  
Vol 31 (12) ◽  
pp. 1882-1890 ◽  
Author(s):  
David J. Papke ◽  
Jonathan A. Nowak ◽  
Matthew B. Yurgelun ◽  
Alexander Frieden ◽  
Amitabh Srivastava ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mismatch Repair ◽  
Colorectal Adenocarcinoma ◽  
Next Generation ◽  
Mismatch Repair Deficiency ◽  
Targeted Next Generation Sequencing ◽  
Repair Deficiency ◽  
Generation Sequencing

scholarly journals Molecular and clinical analysis of 27 German patients with Leber congenital amaurosis

2018 ◽  
Author(s):  
Nicole Weisschuh ◽  
Britta Feldhaus ◽  
Muhammad Imran Khan ◽  
Frans P. M. Cremers ◽  
Susanne Kohl ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Diagnosis ◽  
Detection Rate ◽  
Cost Effective ◽  
Clinical Analysis ◽  
Severe Form ◽  
Next Generation ◽  
Leber Congenital Amaurosis ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

AbstractLeber congenital amaurosis (LCA) is the earliest and most severe form of all inherited retinal dystrophies (IRD) and the most frequent cause of inherited blindness in children. The phenotypic overlap with other early-onset and severe IRDs as well as difficulties associated with the ophthalmic examination of infants can complicate the clinical diagnosis. To date, 25 genes have been implicated in the pathogenesis of LCA. The disorder is usually inherited in an autosomal recessive fashion, although rare dominant cases have been reported. We report the mutation spectra and frequency of genes in 27 German index patients initially diagnosed with LCA. A total of 108 LCA- and other genes implicated in IRD were analysed using a cost-effective targeted next-generation sequencing procedure based on molecular inversion probes (MIPs). Sequencing and variant filtering led to the identification of putative pathogenic variants in 25 cases, thereby leading to a detection rate of 93%. The mutation spectrum comprises 34 different alleles, 17 of which are novel. In line with previous studies, the genetic results led to a revision of the initial clinical diagnosis in a substantial proportion of cases, demonstrating the importance of genetic testing in IRD. In addition, our detection rate of 93% shows that MIPs are a cost-efficient and sensitive tool for targeted next-generation sequencing in IRD.

ERBB3-Activating Mutations in Small Bowel Adenocarcinomas

2018 ◽  
pp. 1-9
Author(s):  
Luc Cabel ◽  
Thomas Aparicio ◽  
Ivan Bieche ◽  
Magali Svrcek ◽  
Aziz Zaanan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Small Bowel ◽  
High Rate ◽  
Clinical Activity ◽  
Tumor Type ◽  
Small Bowel Adenocarcinoma ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Activating Mutations ◽  
Generation Sequencing

Purpose Functional studies have demonstrated that some mutations of ERBB3, which encodes for human epidermal growth factor receptor (HER) 3, are oncogenic via activation of the ErbB family signaling pathway. Significant clinical activity of anti-HER2 therapies (trastuzumab plus lapatinib combination or afatinib) has been reported in patients with ERBB3-mutated cancers. This study was designed to report the rate of activating ERBB3 mutations in small bowel adenocarcinoma (SBA), a rare tumor type in which we previously reported a high rate (12%) of ERBB2-activating mutations. Materials and Methods DNA from 74 SBAs, previously characterized for ERBB2 mutations and mismatch repair status, was submitted for sequencing of ERBB3 exons 3, 6, 7, 8, and 23. Orthogonal validation by targeted next-generation sequencing was performed. Results Four of 74 SBAs (5.4%) displayed ERBB3-activating mutations, including three p.V104M mutations (c.310 G>A) in exon 3 and one p.E928G mutation (c.2783 A>G) in exon 23. No mutations were detected in exons 6, 7, and 8. ERBB3-activating mutations were associated with microsatellite instability ( P = .002) and the presence of ERBB2-activating mutations ( P = .002). Two SBAs with co-occurrence of ERBB2 and ERBB3 mutations were further analyzed by targeted next-generation sequencing. Mutant allelic frequencies suggested that both mutations were shared by the same clone rather than being harbored by mutually exclusive tumor subclones. Conclusion SBAs display a high rate of ERBB3-activating mutations, which have been shown to be targetable by anti-HER2 therapies. Strikingly, ERBB3 was frequently comutated with ERBB2, suggesting a strong oncogenic addiction of these SBAs to the HER2 pathway.

Genetic analysis of hereditary angioedema in a Brazilian family by targeted next generation sequencing

2016 ◽  
Vol 397 (4) ◽  
pp. 315-322 ◽  
Author(s):  
Camila Lopes Veronez ◽  
Elton Dias da Silva ◽  
Patrícia Varela Lima Teixeira ◽  
Nathália Cagini ◽  
Rosemeire Navickas Constantino-Silva ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hereditary Angioedema ◽  
Wide Spectrum ◽  
Cost Effective ◽  
Patient Specific ◽  
Next Generation ◽  
Coding Region ◽  
Software Analysis ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

Abstract Hereditary angioedema (HAE) is accompanied by an overproduction of bradykinin (BK) as the primary mediator of swelling. Although many proteins may be involved in regulating the wide spectrum of HAE symptoms, most studies have only focused on C1-INH and FXII. For the first time, a next generation sequencing (NGS) method was applied to develop a robust, time- and cost-effective diagnostic and research tool to analyze selected genes related to HAE. The entire coding region and the exon-intron boundaries of 15 genes from 23 subjects of a Brazilian family, nine of whom were symptomatic, were analyzed by NGS. One new mutation found uniquely in the nine symptomatic patients, p.Ala457Pro in the SERPING1 gene, was estimated as likely to be pathogenic (PolyPhen-2 software analysis) and is the main candidate to be responsible for HAE in these patients. Alterations identified in a few asymptomatic individuals but also found in almost all symptomatic patients, such as p.Ile197Met (HMWK), p.Glu298Asp (NOS3) and p.Gly354Glu (B2R), may also be involved in modulating patient-specific symptoms. This NGS gene panel has proven to be a valuable tool for a quick and accurate molecular diagnosis of HAE and efficient to indicate modulators of HAE symptoms.

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