Cancer Genetics最新文献_第7页

30. Current next generation sequencing reporting practices: A GOAL Consortium report 30.下一代测序报告的现行做法：GOAL 联合会报告

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.032

Celeste Eno , Rama Sompallae , T. Niroshi Senaratne

{"title":"30. Current next generation sequencing reporting practices: A GOAL Consortium report","authors":"Celeste Eno , Rama Sompallae , T. Niroshi Senaratne","doi":"10.1016/j.cancergen.2024.08.032","DOIUrl":"10.1016/j.cancergen.2024.08.032","url":null,"abstract":"<div><div>Molecular testing by next generation sequencing (NGS) panels are widely used for oncology specimens; however, the reporting of the results vary greatly across institutions. A 70-question survey was sent to member laboratories in the Genomics Organization for Academic Laboratories (GOAL) consortium to assess current reporting practices to assess the potential for standardization. GOAL is a non-profit organization with aims of cross-institutional collaborations, including shared assay content and interpretative frameworks, to allow for academic laboratory success. Each laboratory had the opportunity to fill out the survey for hematological and solid tumor-based panels or a combined survey for both types of tumors. A total of 28 surveys were received from 21 academic tertiary-care laboratories regarding NGS reporting practices. Only a few practices differed significantly between heme and solid tumor panels, including repeat testing. Most notably, the survey respondents noted the time and review process for testing was formidable, including review of previous results, care in reporting potential germline findings, and integrating other ancillary testing. Through these efforts, GOAL seeks to bridge the gap in result reporting, ultimately improving consistency and accuracy of NGS-based molecular testing for cancer. We anticipate the results of this study will help serve as a benchmark for clinical laboratories looking to compare practices with their peers and reveal potential areas for standardization or improvement of clinical reporting.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Page S10"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

35. Integrated comprehensive genomic profiling of meningiomas: A single institutional study 35.脑膜瘤的综合全面基因组图谱分析：单一机构研究

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.037

Mohana Priya Jayavel, Ha Nguyen, Madina Sukhanova, Lucas Santana dos Santos, Behtash Nezami, Juehua Gao, Erica Vormittag-Nocito, Lawrence Jennings, Xinyan Lu

{"title":"35. Integrated comprehensive genomic profiling of meningiomas: A single institutional study","authors":"Mohana Priya Jayavel, Ha Nguyen, Madina Sukhanova, Lucas Santana dos Santos, Behtash Nezami, Juehua Gao, Erica Vormittag-Nocito, Lawrence Jennings, Xinyan Lu","doi":"10.1016/j.cancergen.2024.08.037","DOIUrl":"10.1016/j.cancergen.2024.08.037","url":null,"abstract":"<div><div>Meningioma is the most common central nervous system tumor and understudied because of its benign nature. High-grade meningiomas often show poorer outcome and enriched with high-risk copy-number-aberrations (CNAs) including losses/segmental-losses of chromosomes 1p, 3p, 4p/q, 6p/q, 10p/q, 14q, 18p/q and 19p/q, CDKN2A/B homozygous-deletion (CDKN2A/B-homo) and TERT promoter-mutation (TERTp) detected by comprehensive genomic profiling (CGP) including SNP-microarray, next generation sequencing (NGS) and DNA-methylation. In this study, we performed CGP on a large series of meningioma.</div><div>We identified 122 (45.2%) cases with high-risk CNAs in 270 cases assessed, including 33 WHO-grade-I, 67 WHO-grade-II and 22 WHO-grade-III. Fifty-one (41.8%) cases had hypodiploidy characterized by losses of 22, 14, 10, X/Y, 6 and 8; Eighteen (14.8%) showed polyploidy with relative losses of 1p, 14, 18, 6 and 10. In 53 (43.4%) cases with near-diploidy, half showed complex CNAs with losses/segmental-losses involving 1p, 3p, 19p,14q and 6q. Five cases (4.1%) showed CDKN2A/B-homo. NGS performed in 30 cases revealed mutations in NF2 (n=20), ARID1A (n=7), MSH6 (n=4). Seven (6.6%, 7/106) had TERTp mutation. Methylation profiling matched classifier for meningioma in 92% (79/86) of cases tested. CGP upgraded 58% WHO-grade-I and 67.2% WHO-grade-II tumors to WHO-grade-II and III, respectively. Although follow-up data is limited, 51 patients (41.8%) had tumor recurrence.</div><div>Our study showed that meningiomas are enriched by high-risk CNAs even in low-grade tumors, less frequent TERTp mutation or CDKN2A/B-homo. CGP is of clinical importance for tumor molecular characterizations. CGP should be utilized clinically and integrated in future WHO classifications for tumor grading and risk stratification.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Page S11"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

55. Advancing bladder carcinoma diagnosis: The innovative potential of the BCDx multi-omics approach 55.推进膀胱癌诊断：BCDx 多组学方法的创新潜力

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.057

Thakshila Habarakada Liyanage, Asel Habarakada Liyanage

{"title":"55. Advancing bladder carcinoma diagnosis: The innovative potential of the BCDx multi-omics approach","authors":"Thakshila Habarakada Liyanage, Asel Habarakada Liyanage","doi":"10.1016/j.cancergen.2024.08.057","DOIUrl":"10.1016/j.cancergen.2024.08.057","url":null,"abstract":"<div><div>The use of multi-omic biomarkers in liquid biopsies is emerging as a promising method for enhancing disease detection accuracy. However, it faces significant challenges, such as the complexity of integrating and interpreting data from various omic layers, which is time-consuming, low-throughput, and costly. Additionally, there is currently no simple instrument capable of detecting all the omics simultaneously. Early Is Good (EIG) has developed the Multi-Omic Integration Platform (MIP) to tackle these challenges in early disease detection. MIP can detect DNA, RNA, and proteins simultaneously using a standard plate reader, employing localized surface plasmon resonance (LSPR) of gold nanoparticles to enhance the bioluminescence resonance energy transfer (BRET) readout signal.</div><div>The novel MIP assay technology is applied to early bladder cancer recurrence monitoring using a multi-omic biomarker panel that includes miRNA, mRNA, lncRNA, and proteins. Current methods for identifying bladder cancer (BC) involve cystoscopy and urinary cytology. Cystoscopy, with 97% sensitivity for high-grade tumors, is invasive, operator-dependent, and costly. It often misses small or carcinoma in situ tumors, which can progress to muscle-invasive bladder cancer (MIBC) in about half of the patients. It also causes side effects like dysuria (50%), hematuria (19%), and urinary tract infections (3%), leading to discomfort, anxiety, and embarrassment. Urinary cytology, with 80-90% sensitivity and 98-100% specificity for high-grade tumors, struggles with low sensitivity (4-31%) for low-grade tumors and has a higher rate of false positives. This highlights the need for innovative approaches like the MIP, which offers non-invasive, highly sensitive, and comprehensive detection capabilities, potentially transforming the clinical management of bladder cancer. MIP has shown 100% sensitivity and 100% NPV for bladder cancer recurrence monitoring by combining the multi-omic biomarkers.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Page S18"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

46. Clinical SNP-array adds value to diagnosis and surveillance of bone marrow failure syndromes 46.临床 SNP 阵列为骨髓衰竭综合征的诊断和监测增添价值

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.048

Lucilla Pizzo , Jian Zhao , Akiko Shimamura , Sara Lewis , Marcin Wlodarski , Bo Hong , Erica Andersen

{"title":"46. Clinical SNP-array adds value to diagnosis and surveillance of bone marrow failure syndromes","authors":"Lucilla Pizzo , Jian Zhao , Akiko Shimamura , Sara Lewis , Marcin Wlodarski , Bo Hong , Erica Andersen","doi":"10.1016/j.cancergen.2024.08.048","DOIUrl":"10.1016/j.cancergen.2024.08.048","url":null,"abstract":"<div><div>Cytogenomic SNP microarray (SNP-A) utilization for diagnosis and monitoring of bone marrow failure syndromes (BMFS) is increasing. Understanding the biology of these heterogeneous diseases is required to appropriately identify, interpret, and track prognostically significant clones, some of which may represent revertant somatic genetic rescue (SGR) events. We reviewed SNP-A findings from our encounter of over 100 BMFS cases tested at our institution. Abnormal results were reported in 30 cases, including nine aplastic anemia (AA, 30%), eleven Shwachman-Diamond syndrome (SDS, 37%), six SAMD9/SAMD9L-related syndrome (20%), and four Diamond-Blackfan anemia (DBA, 13%) cases. In 15 (50%) cases, the SNP-A profile was consistent with SGR and acquired correction of the disease-causing variant. Isolated CN-LOH of the chromosome containing the disease-causing gene was observed in 12 (40%) cases, including CN-LOH 7q in two individuals with SDS (SBDS gene) and three individuals with SAMD9/SAMD9L-associated syndromes, and CN-LOH 2p and 19q in two individuals with RPS7 and RPS19-associated DBA, respectively. SGR-associated CNVs included isochromosome 7q (SBDS) and 20q deletion (EIF6 gene) in three cases of SDS. Malignant transformation SNP-A findings were observed in 4/30 (13%) cases, including CN-LOH 17p with TP53 Tier 1 variant in an SDS case and monosomy 7 in three cases of SAMD9/SAMD9L-related syndromes. Concurrent review of cytogenetic/FISH, NGS, and/or germline BMFS results, where available; identification of low-level, complex and/or coexisting clones; and accurate clonal estimation for sequential tracking are essential, and add value to clinical management. Our results emphasize the value of SNP-A in the diagnosis, prognosis, and monitoring of BMFS.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Page S15"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

77. dic(7;9):A distinct entity in B-ALL with multiple genomic aberrations including IKAROS and PAX5 DIC(7;9)：B-ALL 中的一个独特实体，具有多种基因组畸变，包括 IKAROS 和 PAX5

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.079

Ashwini Yenamandra, Rebecca Smith, Kun Zhao, Yingda Wang, Brianna Smith, Christine Smith, Meng-Chang Hsiao, Debra Friedman

{"title":"77. dic(7;9):A distinct entity in B-ALL with multiple genomic aberrations including IKAROS and PAX5","authors":"Ashwini Yenamandra, Rebecca Smith, Kun Zhao, Yingda Wang, Brianna Smith, Christine Smith, Meng-Chang Hsiao, Debra Friedman","doi":"10.1016/j.cancergen.2024.08.079","DOIUrl":"10.1016/j.cancergen.2024.08.079","url":null,"abstract":"<div><div>dic(7;9) is a rare (<1%) and recurrent abnormality in both pediatric and adult B-ALL, resulting in partial monosomy of chromosomes 7p and 9p. Co-occurrence of dic(7;9) with <em>PAX5</em> gene alterations including deletions, mutations and amplification have been reported. <em>PAX5</em> encodes the B lymphoid transcription factor gene that is important in regulating B cell lineage differentiation, leading to B-cell development and may play a crucial role in B lymphoid leukemogenesis.</div><div>Here, we present two cases of pediatric B-ALL with dic(7;9) with complex genomic aberrations.</div><div>Case 1: is a four year old female who presented in 2024 with orbital and left sinus maxillary masses, anemia, fever and leukocytosis with peripheral blasts. Karyotype and fish were complex with 45,XX,der(7)dic(7;9)(p11.2;p13)del(7)(p13p11.2)t(7;20)(p13;q11.2),der(20)t(7;20)(p13;q11.2)[13]/46,XX[7]. SNP array revealed loss of 7p and 9p including <em>IKAROS</em> and <em>PAX5</em>, respectively.</div><div>Cerebral sinus fluid demonstrated a leukocytosis with leukemic blasts, resulting in a CNS3b classification. She had negative minimal residual disease at the end of induction on a very high-risk standard of care protocol and on consolidation therapy.</div><div>Case 2: is a 10 year old male referred in 2022 for a month of fever and fatigue.. karyotype was complex with several rearrangements. 45,XY,dic(7)t(7;9)(p13;p13),-9,der(10)t(9;10)(q34.1;q22),der(12)t(7;12)(p13;p13),der(13)t(10;13)(q22;q34)[11]/46,XY[9].</div><div>The patient was treated on a standard risk standard of care protocol and had negative minimal residual disease at the end of induction. He remains in remission during maintenance therapy.</div><div>Given the two dic (7;9) cases described here have complex karyotypes, it is possible that <em>PAX5</em> and <em>IKZF1</em> alterations may be contributing to this complex cytogenetic entity.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Pages S24-S25"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

6. Hot-spot D816 KIT has different clinical outcome compared to non-D816 KIT variants in myeloid neoplasms 6.与非 D816 KIT 变体相比，骨髓性肿瘤中的热点 D816 KIT 具有不同的临床结果

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.008

Barina Aqil , Lucas Santana-Santos , Juehua Gao , Xinyan Lu , Amandeep Kaur , Erica Vormittag-Nocito , Lawrence Jennings , Yasmin Abaza , Madina Sukhanova

{"title":"6. Hot-spot D816 KIT has different clinical outcome compared to non-D816 KIT variants in myeloid neoplasms","authors":"Barina Aqil , Lucas Santana-Santos , Juehua Gao , Xinyan Lu , Amandeep Kaur , Erica Vormittag-Nocito , Lawrence Jennings , Yasmin Abaza , Madina Sukhanova","doi":"10.1016/j.cancergen.2024.08.008","DOIUrl":"10.1016/j.cancergen.2024.08.008","url":null,"abstract":"<div><div><em>KIT</em> (proto-oncogene) plays significant role in diagnosis and prognosis of myeloid neoplasms (MNs). The hot-spot <em>KIT</em> D816 mutation in exon 17 is recognized by WHO classification as poor prognostic marker for acute myeloid leukemia (AML) with <em>RUNX1::RUNX1T1</em> and as one of diagnostic and prognostic criteria for systemic mastocytosis (SM), a MN characterized by clonal proliferation of mast cells. The role of activating <em>KIT</em> mutations outside of codon 816 was recognized, resulting in addition of few critical <em>KIT</em> regions in updated consensus proposal for SM diagnosis. However, information on prognostic weight of these 'non-hot-spot' changes is limited. Here we present results of comparative analysis of clinicopathological and survival parameters for patients diagnosed with MNs with activating <em>KIT</em> changes outside of codon 816 (N=14) using patients with MNs with <em>KIT</em> D816 (N=26) as comparative group. Most of study patients had AML (65%) followed by MDS and MDS/MPN (35% combined). Both study groups had same representation of normal, non-complex and complex karyotypes, and karyotypes with diagnostic t(8;21) and inv(16). IHC staining for c-KIT (CD117) detected significantly lower percentage of mast cells with c-Kit protein expression in non-D816 group in contrast to patients with D816 <em>KIT</em> (p<0.0076). Consistent with that, none of the non-D816 group patients developed SM compared to 31% of D816 group patients who developed SM. Notably, the group with non-D816 <em>KIT</em> showed better OS compared to patients with D816 change (p<0.016). Our results support the hypothesis of weaker prognostic impact of non-D816 <em>KIT</em> mutations compared to D816 hot-spot.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Pages S2-S3"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A complex t(15;22;17)(q22;q11.2;q21) variant of APL APL 的复杂 t(15;22;17)(q22;q11.2;q21)变体

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.07.003

Bilgesu Ak , Özge Güngör , Emin Karaca , Burak Durmaz , Denis S. Bozer , Mahmut Töbü , Haluk Akın

{"title":"A complex t(15;22;17)(q22;q11.2;q21) variant of APL","authors":"Bilgesu Ak , Özge Güngör , Emin Karaca , Burak Durmaz , Denis S. Bozer , Mahmut Töbü , Haluk Akın","doi":"10.1016/j.cancergen.2024.07.003","DOIUrl":"10.1016/j.cancergen.2024.07.003","url":null,"abstract":"<div><p>The present study described an extremely rare case of acute promyelocytic leukemia (APL) characterized by a complex three‑way (15;22;17)(q22;q11.2;q21) translocation. Acute promyelocytic leukemia (APL) is a specific subtype of acute myeloid leukemia with distinctive clinical and therapeutic characteristics. Besides being characterized by the t(15;17)(q22;q12) translocation, this subtype is also notable for its response to all-trans-retinoic acid (ATRA) treatment. APL is highly responsive to a combination of ATRA and chemotherapeutic agents, achieving over 90 % complete remission rates and over 80 % long-term remission rates. In this case, a 79-year-old male patient presented with complaints of weakness, fatigue, and petechial rash, with no other significant medical history except for diabetes mellitus and hypertension. Conventional cytogenetic methods, dual-color dual-fusion, and dual-color break-apart fluorescent in situ hybridization techniques together identified the t(15;22;17) translocation. RT-PCR analysis was performed for expression of PML/RARA fusion transcripts. The patient, diagnosed with APL, exhibited a complete response to all-trans retinoic acid (ATRA) and idarubicin treatment. In this paper, we present the second documented case of t(15;22;17) and explore the remarkable remission observed following treatment with All-Trans Retinoic Acid (ATRA).</p></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Pages 48-51"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141839783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

4. The clinical implementation of technologies utilized for macrogenomic event detection in solid tumors 4.实体瘤宏基因组事件检测技术的临床应用

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.006

Lisa Lansdon , Laveniya Satgunaseelan , Xiangqiang Shao , Cynthia Chow , Trevor Pugh , Gokce Toruner

{"title":"4. The clinical implementation of technologies utilized for macrogenomic event detection in solid tumors","authors":"Lisa Lansdon , Laveniya Satgunaseelan , Xiangqiang Shao , Cynthia Chow , Trevor Pugh , Gokce Toruner","doi":"10.1016/j.cancergen.2024.08.006","DOIUrl":"10.1016/j.cancergen.2024.08.006","url":null,"abstract":"<div><div>Macrogenomic events (MGE) are large genomic alterations that together contribute to complex, genome-wide mutational or structural signatures. These include aneuploidy, structural variants, changes in copy number, regions of copy neutral loss of heterozygosity, mutation signatures, homologous recombination deficiency, and microsatellite instability. Although there are several existing and emerging technologies for the detection of MGE, limited work has been done to systematically assess their utility within solid tumor testing. Thus, we formed the CGC MGE Working Group to summarize the strengths and limitations of various technologies for solid tumor MGE detection at multiple resolutions, to evaluate those in current clinical use, and to provide an assessment of feasibility of clinical implementation for newer assays. Technologies under consideration are whole genome sequencing (short- and long-read), optical genome mapping, microarray (chromosomal and methylation), karyotyping, targeted sequencing technologies (i.e., Sanger, ddPCR, qPCR, targeted sequencing panels), FISH, and Hi-C. Through a review of the literature and local laboratory protocols, we defined 15 data capture criteria by which each of these tests are being assessed, ranging from sample requirements (e.g., fresh-frozen versus formalin-fixed paraffin embedded tissue), to breakpoint precision and the types of MGE detected. Although this effort is ongoing, preliminary findings suggest that while a 'perfect' test menu may not exist, common indications for testing and existing laboratory infrastructure may help determine test prioritization. In addition, our group identified several barriers to solid tumor testing (e.g., percent tumor requirements, precision of breakpoints required, RNA vs DNA-based testing) to consider when assessing overall clinical utility.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Page S2"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

26. Classifying the oncogenicity of 100 variants from pediatric cancer patients using a standardized assessment framework 26.使用标准化评估框架对来自儿科癌症患者的 100 个变异体的致癌性进行分类

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.028

Wesley Goar , Kori Kuzma , Kathryn Stahl , Kathleen Schieffer , Catherine Cottrell , Elaine Mardis , Alex Wagner

{"title":"26. Classifying the oncogenicity of 100 variants from pediatric cancer patients using a standardized assessment framework","authors":"Wesley Goar , Kori Kuzma , Kathryn Stahl , Kathleen Schieffer , Catherine Cottrell , Elaine Mardis , Alex Wagner","doi":"10.1016/j.cancergen.2024.08.028","DOIUrl":"10.1016/j.cancergen.2024.08.028","url":null,"abstract":"<div><div>The ClinGen/CGC/VICC Oncogenicity guidelines were published in 2022 as a standardized approach for assessing a variant's capacity to promote cancer formation. We describe an assessment tool, the Variation Categorizer (VarCat), that creates highly-structured oncogenicity classifications following these guidelines suitable for a clinical laboratory setting through an intuitive user-facing web application. The resulting classification is stored in a standardized genomic knowledge format developed by the Global Alliance for Genomics and Health (GA4GH) to promote interoperability and data sharing.</div><div>Here we report our assessment of 100 somatic variants from pediatric cancer cases studied by NGS-based exome sequencing in comparison to prior assessments characterized under the AMP/ASCO/CAP clinical actionability guidelines. Our study assesses application of these complementary guidelines in a high-throughput clinical setting. We describe the frequency and impact of specific oncogenicity codes used in these variant classification assessments. Our findings highlight specific codes that would benefit from further clarification for application to clinical classification workflows pursuant to clinical testing. Of particular note, we discuss applications of the OP2 (single genetic etiology) code and the need for objective criteria that classify cited studies as providing well-established, reproducible, and robust evidence. We present the challenges created due to these subjective guidelines and present our internal framework for systematically applying these codes. We conclude with an overview of the impact of our revised assessment criteria on interpretation turn-around time and reproducibility.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Page S9"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

29. Reimbursement for molecular pathology testing for neoplasia: The 2024 update 29.肿瘤分子病理学检测的报销：2024 年的更新

IF 1.4 4区医学

Cancer Genetics Pub Date : 2024-08-01 DOI: 10.1016/j.cancergen.2024.08.031

Xiaoyu Qu, Melissa Chiu, Serena Ruffino, Barrett Walker, Kate Kroeger, Min Fang

{"title":"29. Reimbursement for molecular pathology testing for neoplasia: The 2024 update","authors":"Xiaoyu Qu, Melissa Chiu, Serena Ruffino, Barrett Walker, Kate Kroeger, Min Fang","doi":"10.1016/j.cancergen.2024.08.031","DOIUrl":"10.1016/j.cancergen.2024.08.031","url":null,"abstract":"<div><div>Chromosome genomic array testing (CGAT), targeted mutation NGS, and targeted RNA sequencing (TRS) are incorporated in the pathway testing scheme for hematologic disorders at our institution. Previously, we shared the reimbursement landscape of CGAT and mutation NGS for FY-17. Here we present an update for FY-18 to FY-23, encompassing CGAT (HCPCS 81406 and 81277), mutation NGS (81450 and 81455), and TRS (81455). Compared with FY-17, FY-18 to FY-23 showed improved percent of cases reimbursed for CGAT. Six-year average percentage of cases reimbursed showed 68% (yearly range: 58% to 80%) for CGAT, 74% (69% to 92%) for mutation NGS under 81450, and 76% (50% to 81%) for mutation NGS and TRS under 81455. The percentage of cases reimbursed varied between payers: CGAT/NGS had 82%/71% by commercial payers, 65%/70% by Medicaid, and 53%/83% by Medicare. The payer mix varied between years with the median payer percentage of commercial payers at 52% (45 to 57%), Medicare at 32% (25 to 45%), and Medicaid at 11% (7 to 15%). Out of 33 TRS studies billed, 20 cases were reimbursed (61%), including 9 out of 11 (82%) by commercial, 7 out of 14 (50%) by Medicare, and 4 out of 5 by Medicaid (80%). In conclusion, our assessment of percentage of claims receiving payment suggests improved reimbursement landscape for molecular assays over time with a trend showing more success with commercial payers than Medicare and Medicaid as well as higher percentage of cases being reimbursed for mutation NGS than for CGAT.</div></div>","PeriodicalId":49225,"journal":{"name":"Cancer Genetics","volume":"286 ","pages":"Pages S9-S10"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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