A novel B*07 variant allele, B*07:416 , identified by next‐generation sequencing

HLA ◽  
2021 ◽  
Author(s):  
Mei San Tang ◽  
Brian F. Duffy ◽  
Jo‐Ellen Jennemann ◽  
Bijal A. Parikh ◽  
Chang Liu
Keyword(s):  
Next Generation Sequencing ◽  
Variant Allele ◽  
Next Generation ◽  
Generation Sequencing

Identification of a novel HLA‐DQB1*05 variant allele, HLA‐DQB1*05:247 by next‐generation sequencing

HLA ◽  
2020 ◽  
Vol 96 (2) ◽  
pp. 242-243 ◽  
Author(s):  
Shinae Yu ◽  
Hae Jung Bae ◽  
So‐Jung Choi ◽  
Kyung Ran Jun
Keyword(s):  
Next Generation Sequencing ◽  
Variant Allele ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Proficiency Testing of Standardized Samples Shows Very High Interlaboratory Agreement for Clinical Next-Generation Sequencing–Based Oncology Assays

2018 ◽  
Vol 143 (4) ◽  
pp. 463-471 ◽  
Author(s):  
Jason D. Merker ◽  
Kelly Devereaux ◽  
A. John Iafrate ◽  
Suzanne Kamel-Reid ◽  
Annette S. Kim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Proficiency Testing ◽  
False Negative ◽  
High Specificity ◽  
Variant Allele ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Sequencing Platform ◽  
Negative Results ◽  
Generation Sequencing

Context.— Next-generation sequencing–based assays are being increasingly used in the clinical setting for the detection of somatic variants in solid tumors, but limited data are available regarding the interlaboratory performance of these assays. Objective.— To examine proficiency testing data from the initial College of American Pathologists (CAP) Next-Generation Sequencing Solid Tumor survey to report on laboratory performance. Design.— CAP proficiency testing results from 111 laboratories were analyzed for accuracy and associated assay performance characteristics. Results.— The overall accuracy observed for all variants was 98.3%. Rare false-negative results could not be attributed to sequencing platform, selection method, or other assay characteristics. The median and average of the variant allele fractions reported by the laboratories were within 10% of those orthogonally determined by digital polymerase chain reaction for each variant. The median coverage reported at the variant sites ranged from 1922 to 3297. Conclusions.— Laboratories demonstrated an overall accuracy of greater than 98% with high specificity when examining 10 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 15% or greater. These initial data suggest excellent performance, but further ongoing studies are needed to evaluate the performance of lower variant allele fractions and additional variant types.

scholarly journals Proficiency Testing of Standardized Samples Shows High Interlaboratory Agreement for Clinical Next-Generation Sequencing–Based Hematologic Malignancy Assays With Survey Material–Specific Differences in Variant Frequencies

2020 ◽  
Vol 144 (8) ◽  
pp. 959-966 ◽  
Author(s):  
Alissa Keegan ◽  
Julia A. Bridge ◽  
Neal I. Lindeman ◽  
Thomas A. Long ◽  
Jason D. Merker ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Proficiency Testing ◽  
Hematologic Malignancy ◽  
False Negative ◽  
False Negative Rate ◽  
Hematologic Malignancies ◽  
Variant Allele ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Generation Sequencing

Context.— As laboratories increasingly turn from single-analyte testing in hematologic malignancies to next-generation sequencing–based panel testing, there is a corresponding need for proficiency testing to ensure adequate performance of these next-generation sequencing assays for optimal patient care. Objective.— To report the performance of laboratories on proficiency testing from the first 4 College of American Pathologists Next-Generation Sequencing Hematologic Malignancy surveys. Design.— College of American Pathologists proficiency testing results for 36 different engineered variants and/or allele fractions as well as a sample with no pathogenic variants were analyzed for accuracy and associated assay performance characteristics. Results.— The overall sensitivity observed for all variants was 93.5% (2190 of 2341) with 99.8% specificity (22 800 of 22 840). The false-negative rate was 6.5% (151 of 2341), and the largest single cause of these errors was difficulty in identifying variants in the sequence of CEBPA that is rich in cytosines and guanines. False-positive results (0.18%; 40 of 22 840) were most likely the result of preanalytic or postanalytic errors. Interestingly, the variant allele fractions were almost uniformly lower than the engineered fraction (as measured by digital polymerase chain reaction). Extensive troubleshooting identified a multifactorial cause for the low variant allele fractions, a result of an interaction between the linearized nature of the plasmid and the Illumina TruSeq chemistry. Conclusions.— Laboratories demonstrated an overall accuracy of 99.2% (24 990 of 25 181) with 99.8% specificity and 93.5% sensitivity when examining 36 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 10% or greater. The data also highlight an issue with artificial linearized plasmids as survey material for next-generation sequencing.

Characterization of advanced hepatocellular carcinoma patients via a multi-omic cancer registry.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16617-e16617
Author(s):  
Joseph S Ryan ◽  
Xiaojun Xu ◽  
Pablo Tamayo ◽  
Adam Burgoyne
Keyword(s):  
Hepatocellular Carcinoma ◽  
Next Generation Sequencing ◽  
Cancer Registry ◽  
Tumor Tissue ◽  
Response To Therapy ◽  
Variant Allele ◽  
Advanced Hepatocellular Carcinoma ◽  
Next Generation ◽  
Tumor Tissues ◽  
Generation Sequencing

e16617 Background: Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver and has significant cancer-related mortality worldwide. Molecularly matched therapy has an emerging role in HCC treatment; however, HCC poses a unique challenge as patients are frequently diagnosed radiographically rather than by tissue biopsy, limiting our ability to utilize tumor tissue data for therapy selection. The purpose of this study is to establish a multi-omic database with matched demographic and clinical data to identify patterns of shared molecular aberrations in HCC tumors. Methods: An institutional HCC cancer registry was created, and a retrospective review was performed using data from 2017-2020 at a tertiary cancer center. 56 patients with advanced HCC were identified, and tissue samples were analyzed with multi-omic profiling assays (next generation DNA sequencing, RNA sequencing, protein expression via immunohistochemistry) versus ctDNA from peripheral blood. Results: Next generation sequencing was obtained for 38 (76%) patients using either tissue or ctDNA. While the results were similar, a higher number of total mutations were identified using tumor tissues rather than ctDNA. The average variant allele fraction for tumor tissues was approximately 10x higher than the variant allele fractions identified by ctDNA. However, ctDNA sequencing identified a higher number of potentially actionable mutations, on average, than did tissue testing. The most commonly mutated genes included TERT (42% of patients), TP53 (47%), CTNNB1 (34%), ARID1A (18%), CCND1 (16%), and NEF2L2 (13%). Several patients had serial ctDNA sequencing, which showed an increase in actionable and total mutations over time as well as changes in variant allele fractions in response to therapy. Conclusions: Next generation sequencing of ctDNA can be used in lieu of tumor tissue in patients diagnosed with HCC radiographically to identify actionable mutations, but it may underestimate the mutational burden of HCC tumors. Serial analyses with cell free DNA may be useful to monitor clonal evolution in response to targeted treatment and may identify new actionable mutations as patients progress on systemic therapies. [Table: see text]

Identification of a novel HLA‐B*40 variant allele, B*40:405 by next‐generation sequencing

HLA ◽  
2019 ◽  
Vol 93 (6) ◽  
pp. 491-492 ◽  
Author(s):  
Shinae Yu ◽  
Jae Houn Shim ◽  
Kwang Jun Park ◽  
So‐Jung Choi ◽  
Kyung Ran Jun
Keyword(s):  
Next Generation Sequencing ◽  
Variant Allele ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-generation sequencing of 35 RHD variants in 16 253 serologically D− pregnant women in the Finnish population

2020 ◽  
Vol 4 (20) ◽  
pp. 4994-5001
Author(s):  
Silja M. Tammi ◽  
Wajnat A. Tounsi ◽  
Susanna Sainio ◽  
Michele Kiernan ◽  
Neil D. Avent ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Screening Program ◽  
Polymerase Chain Reaction Amplification ◽  
Variant Allele ◽  
Next Generation ◽  
Finnish Population ◽  
New Information ◽  
Comprehensive Knowledge ◽  
Novel Alleles ◽  
Generation Sequencing

Abstract Fetal RHD screening for targeted routine antenatal anti-D prophylaxis has been implemented in many countries, including Finland, since the 2010s. Comprehensive knowledge of the RHD polymorphism in the population is essential for the performance and safety of the anti-D prophylaxis program. During the first 3 years of the national screening program in Finland, over 16 000 samples from RhD− women were screened for fetal RHD; among them, 79 samples (0.5%) containing a maternal variant allele were detected. Of the detected maternal variants, 35 cases remained inconclusive using the traditional genotyping methods and required further analysis by next-generation sequencing (NGS) of the whole RHD gene to uncover the variant allele. In addition to the 13 RHD variants that have been previously reported in different populations, 8 novel variants were also detected, indicating that there is more variation of RHD in the RhD− Finnish population than has been previously known. Three of the novel alleles were identified in multiple samples; thus, they are likely specific to the original Finnish population. National screening has thus provided new information about the diversity of RHD variants in the Finnish population. The results show that NGS is a powerful method for genotyping the highly polymorphic RHD gene compared with traditional methods that rely on the detection of specific nucleotides by polymerase chain reaction amplification.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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