Targeted Mutation Analysis Research Articles

A significant proportion of classic Hodgkin lymphoma recurrences represents clonally unrelated second primary lymphoma

AbstractDespite high cure rates in classic Hodgkin lymphoma (cHL), relapses are observed. Whether relapsed cHL represents second primary lymphoma or an underlying T-cell lymphoma (TCL) mimicking cHL is underinvestigated. To analyze the nature of cHL recurrences, in-depth clonality testing of immunoglobulin (Ig) and T-cell receptor (TCR) rearrangements was performed in paired cHL diagnoses and recurrences among 60 patients, supported by targeted mutation analysis of lymphoma-associated genes. Clonal Ig rearrangements were detected by next-generation sequencing (NGS) in 69 of 120 (58%) diagnoses and recurrence samples. The clonal relationship could be established in 34 cases, identifying clonally related relapsed cHL in 24 of 34 patients (71%). Clonally unrelated cHL was observed in 10 of 34 patients (29%) as determined by IG-NGS clonality assessment and confirmed by the identification of predominantly mutually exclusive gene mutations in the paired cHL samples. In recurrences of >2 years, ∼60% of patients with cHL for whom the clonal relationship could be established showed a second primary cHL. Clonal TCR gene rearrangements were identified in 14 of 125 samples (11%), and TCL-associated gene mutations were detected in 7 of 14 samples. Retrospective pathology review with integration of the molecular findings were consistent with an underlying TCL in 5 patients aged >50 years. This study shows that cHL recurrences, especially after 2 years, sometimes represent a new primary cHL or TCL mimicking cHL, as uncovered by NGS-based Ig/TCR clonality testing and gene mutation analysis. Given the significant therapeutic consequences, molecular testing of a presumed relapse in cHL is crucial for subsequent appropriate treatment strategies adapted to the specific lymphoma presentation.

Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification.

SARS-CoV-2 variant surveillance informs vaccine composition and decisions to de-authorize antibody therapies. Though detailed genetic characterization requires whole-genome sequencing, targeted mutation analysis may complement pandemic surveillance efforts. This study investigated the qualitative performance of a multiplex oligonucleotide ligation assay targeting 19 spike mutations using 192 whole genome sequenced upper respiratory samples representing SARS-CoV-2 variants of concern. Initial valid results were obtained from 95.8% [95% confidence interval (CI): 92.0 - 98.2; 184/192] of samples. All eight invalid samples were valid on repeat testing. When comparing SARS-CoV-2 oligonucleotide ligase assay SARS-CoV-2 variant calls with whole genome sequencing, overall positive percent agreement was 100% (95% CI: 98.1 - 100.0; 192/192), as was the positive and negative percent agreement for each of the tested variants; Gamma, Delta, Omicron BA.1, BA.2, and BA.4/BA.5. This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.

Artificial Intelligence-Driven Morphology-Based Enrichment of Malignant Cells from Body Fluid

Cell morphology is a fundamental feature used to evaluate patient specimens in pathologic analysis. However, traditional cytopathology analysis of patient effusion samples is limited by low tumor cell abundance coupled with the high background of nonmalignant cells, restricting the ability of downstream molecular and functional analyses to identify actionable therapeutic targets. We applied the Deepcell platform that combines microfluidic sorting, brightfield imaging, and real-time deep learning interpretations based on multidimensional morphology to enrich carcinoma cells from malignant effusions without cell staining or labels. Carcinoma cell enrichment was validated with whole genome sequencing and targeted mutation analysis, which showed a higher sensitivity for detection of tumor fractions and critical somatic variant mutations that were initially at low levels or undetectable in presort patient samples. Our study demonstrates the feasibility and added value of supplementing traditional morphology-based cytology with deep learning, multidimensional morphology analysis, and microfluidic sorting.

Improving the process of ordering outside genomic testing for lung cancer FNA and small biopsy specimens - A multidisciplinary quality improvement project.

Lung cancer is an important cause of mortality in the United States. Targeted mutation analysis has the potential to alter mortality in those with non-small-cell lung cancer. As such, the importance of timely tissue turnaround time (TAT) is substantial. We evaluated TAT at Mayo Clinic Arizona and found it to be delayed relative to national standards. We conducted a series of plan, do, study, and act (PDSA) cycles at a single institution to identify areas for improvement with our lung cancer genomic testing. We assembled a multidisciplinary team and held serial meetings to discuss data from each PDSA cycle. Using PDSA cycles and multidisciplinary discussions, we were able to identify a number of process limitations slowing TAT. We were then able to generate enhanced and timely communication between providers and pathology, educate and enforce the order/requisition workflow, and establish pathology accessioning with lung cancer specimens top priority. We were able to generate and implement a standard operating procedure for genomic testing of lung cancer specimens at our institution, thereby reducing tissue TAT.

Abstract 2392: Multi-dimensional morphology analysis enables identification and label-free enrichment of heterogeneous tumor cell populations

Abstract Studying tumor heterogeneity at single cell resolution is crucial for elucidating tumor progression and treatment response. Classically, tumor cells are characterized with a limited set of biomarkers that cannot cover the full extent of the tumor cell heterogeneity. The advent of single cell genomics has enabled scientists to study heterogeneity at high resolution, but gene expression signatures may not translate to readily available biomarkers for functional studies. Multi-dimensional morphology analysis has the potential for higher resolution than cell surface biomarkers while also reducing cell manipulations. The Deepcell platform enables multi-dimensional morphology analysis of unlabeled single cells using artificial intelligence (AI), imaging, and microfluidics, allowing for higher resolution of population heterogeneity beyond protein expression markers. Using the Deepcell platform, we trained an AI model to identify and sort for malignant cells from non-small cell lung cancer cells (NSCLC) tumor biopsies based on morphology. scRNA-seq, CNV, and targeted mutation analysis verified enrichment of carcinoma cells. Sorted cells had gene expression signatures indicative of tumor cells (e.g. EpCAM expression), increased genomic alterations by CNV analysis, and increased allele frequency of P53 and KRAS mutations relative to pre-sorted samples. Overall, the data indicate brightfield images of cells can be used to detect macro-level changes in cell morphology resulting from the molecular events involved in tumorigenesis. In addition, we induced chemotherapeutic drug resistance of lung cancer cell lines in vitro, imaged the resulting cultures on the Deepcell platform, and used the bright-field cell images to generate multi-dimensional morphological embeddings that can be visualized by UMAP. The resulting UMAPs showed distinct clusters of cells for both the parent and resistant cell lines, indicating that there are morphological differences associated with drug resistance. We developed a random forest classifier to identify the top differential morphological features between parental and resistant cell lines. These top features can distinguish between the populations with high accuracy (87%). Finally, we performed multi-dimensional morphology analysis to compare lung adenocarcinoma (LA) and squamous cell carcinoma (SCC) cell lines. The classifier predicted the correct cell type with 75% accuracy, suggesting that differences between these two carcinomas are reflected in their morphology. Together, our data suggest that AI-detected morphological differences between cell populations may show a biologically significant link between morphology and phenotype. As such, multi-dimensional morphology analysis will bolster the understanding of complex disease states and tumor microenvironment, particularly in patient derived biopsies. Citation Format: Andreja Jovic, Kiran Saini, Ryan Carelli, Tiffine Pham, Christian Corona, Jeanette Mei, Michael Phelan, Stephane C. Boutet, Kevn Jacobs, Julie Kim, Manisha Ray, Chassidy Johnson, Nianzhen Li, Mahyar Salek, Maddison Masaeli, Matt Barnes, Cyril Ramathal. Multi-dimensional morphology analysis enables identification and label-free enrichment of heterogeneous tumor cell populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2392.

A pilot study to evaluate tissue- and plasma-based DNA driver mutations in a cohort of patients with pancreatic intraductal papillary mucinous neoplasms.

Intraductal papillary mucinous neoplasms (IPMNs) are precursor lesions to pancreatic ductal adenocarcinoma that are challenging to manage due to limited imaging, cytologic, and molecular markers that accurately classify lesions, grade of dysplasia, or focus of invasion preoperatively. The objective of this pilot study was to determine the frequency and type of DNA mutations in a cohort of surgically resected, pathologically confirmed IPMN, and to determine if concordant mutations are detectable in paired pretreatment plasma samples. Formalin-fixed paraffin-embedded (FFPE) tissue from 46 surgically resected IPMNs (31 low-grade, 15 high-grade) and paired plasma from a subset of 15 IPMN cases (10 low-grade, 5 high-grade) were subjected to targeted mutation analysis using a QIAseq Targeted DNA Custom Panel. Common driver mutations were detected in FFPE from 44 of 46 (95.6%) IPMN cases spanning all grades; the most common DNA mutations included: KRAS (80%), RNF43 (24%), and GNAS (43%). Of note, we observed a significant increase in the frequency of RNF43 mutations from low-grade to high-grade IPMNs associated or concomitant with invasive carcinoma (trend test, P = 0.01). Among the subset of cases with paired plasma, driver mutations identified in the IPMNs were not detected in circulation. Overall, our results indicate that mutational burden for IPMNs is a common occurrence, even in low-grade IPMNs. Furthermore, although blood-based biopsies are an attractive, noninvasive method for detecting somatic DNA mutations, the QIAseq panel was not sensitive enough to detect driver mutations that existed in IPMN tissue using paired plasma in the volume we were able to retrieve for this retrospective study.

OR20-6 Histopathology and Genetic Causes of Primary Aldosteronism in Young Patients

Abstract Background Primary aldosteronism (PA) is the most common cause of endocrine-related hypertension. However, due to its rare incidence in younger patients, the molecular features of young-onset PA have not been well defined. Recent advances in targeted mutation analysis have identified aldosterone-driver somatic mutations in aldosterone-producing lesions including aldosterone-producing adenomas (APAs) and aldosterone-producing nodules (APNs). Objective To determine the histologic and somatic mutation profile in young-onset PA. Methods Formalin-fixed paraffin-embedded adrenals from 73 patients with unilateral PA (53 women, 19 men, and one with unknown sex) under 35 years old were analyzed. Aldosterone synthase (CYP11B2) immunohistochemistry was used to define the histopathologic classification of the aldosterone-producing lesions based on the HISTALDO consensus as well as guide DNA capture. Somatic mutations were identified by direct Sanger sequencing or Ion Torrent-based targeted next-generation sequencing. Results We identified 48 APAs, 20 APNs, 2 multiple aldosterone-producing nodules (MAPNs), and 3 non-functioning adenomas (NFAs). Of the 45 APAs and 18 APNs with successful sequencing, 43 APAs (96%) and 17 (94%) APNs harbored somatic mutations. The most frequent alterations in APAs were KCNJ5 mutations (35/45, 78%), while CACNA1D mutations were the most common in APNs (8/18, 44%). The mutation prevalence for KCNJ5 mutations did not vary between men and women. In both MAPNs, multiple CYP11B2-expressing lesions shared an identical somatic KCNJ5 mutation (c.451G>A, p.G151R). No somatic mutations were detected in the 3 NFAs. Conclusion APAs are the most common histologic feature of unilateral young-onset PA. Somatic KCNJ5 mutations are more commonly seen in APAs in both men and women, while somatic CACNA1D mutations are frequently seen in APNs in these younger patients. Presentation: Monday, June 13, 2022 12:15 p.m. - 12:30 p.m.

Mutation profiling of the c.1521_1523delCTT (p.Phe508del, F508del) cystic fibrosis transmembrane conductance regulator allele using haplotype-resolved long-read next generation sequencing.

Current approaches to characterize the mutational profile of the cystic fibrosis transmembrane conductance regulator (CFTR) gene are based on targeted mutation analysis or whole gene studies derived from short-read next generation sequencing (NGS). However, these methods lack phasing capability which, in certain scenarios, can provide clinically valuable information. In the present work, we performed near-full length CFTR using Single-Molecule Real-Time Sequencing to produce haplotype-resolved data from both homozygous and heterozygous individuals for mutation c.1521_1523delCTT (p.Phe508del, F508del). This approach utilizes target enrichment of the CFTR gene using biotinylated probes, facilitates multiplexing samples in the same sequencing run, and utilizes fully-automated bioinformatics pipelines for error correction and variant calling. We show a remarkable conservation of F508del haplotype, consistent with the single gene founder effect, as well as diverse mutational profiles in non-F508del alleles. By the same method, 105 single nucleotide polymorphisms (SNPs) exhibiting invariant linkage to F508del CFTR (which better define the founder haplotype) were identified. High level homology between F508del sequences derived from heterozygotes, and those obtained from homozygous individuals, demonstrate accuracy of this method to produce haplotype resolved sequencing. The studies provide a new diagnostic technology for detailed analysis of complex CFTR alleles linked to disease severity.

Targeted Mutation Analysis of Acute Myeloid Leukemia at Diagnosis and Relapse Shows Different Clonal Evolution Patterns Involving Different Functional Classes of Genes

AML relapse is often associated with a clonal evolution at the cytogenetic and molecular level and therefore represents a challenge for the treatment. Targeted sequencing is now usually done at diagnosis in AML, as only a small core group of genes is frequently mutated in AML and MDS. This approach, contrary to Whole Genome Sequencing, is cheaper and allows the detection of variant allele fractions as low as 2% with a rapid turnover and high sequencing coverage and depths.In this study we analyzed the karyotype and the mutations occuring in a panel of genes in 31 AML patients at diagnosis and at the relapse.The Illumina TruSight Myeloid Sequencing Panel® was used that covers all exons of 15 genes and hotspots of 39 additionnal genes involved in myeloid malignancies. Three different pipelines were used for data analysis including GATK, Picard, Samtools, VarScan reference tools. We tried to assess the clonality and the clonal evolution patterns at relapse. Five different clonal evolution patterns including cytogenetic and molecular analyses were observed: (1) Stability, defined by absence of clonal change, (2) Gain, strictly defined by acquisition of additional variations (mutations or cytogenetic alterations), (3) Loss, strictly defined by loss of variants or regression, (4) Gain and Loss, indicating the combination of both “Gain” and “Loss” patterns, (5) Emergence, defined by the emergence of alterations that is unrelated to those found at diagnosis.The cohort included 20 men and 11 women with a median age of 59 years old for which frozen DNA was available both at diagnosis and relapse that were referred in a single center. The elapsed time between the first remission and relapse (TTR) was 1.6 to 113.8 months. Almost all patients relapsed prematurely (less than 12 months). The overall survival and the survival after relapse were respectively 23.7 months and 9.1 months.The cytogenetic evolution patterns observed at relapse were the following: Stability (40%), Gain (27%), Loss (31%), Gain and Loss (4%), Emergence (<1%). The mutation evolution patterns observed at relapse were the following: Stability (26%), Gain (23%), Loss (32%), Gain and Loss (16%), Emergence (3%) . No correlation between cytogenetic and mutation pattern was observed.Patients without change at relapse (“Stability” pattern) had less mutated genes at diagnosis than in the other patterns (p=0.009). Whereas patients with the “Gain and Loss” pattern had more mutated genes at diagnosis than the other patients (≥4 mutated genes, p=0.001). Thirty five percent of the alterations acquired at relapse (“Gain” and “Gain and Loss” patterns) were found in tumor suppressor genes: TP53 was mutated in 60% of these patients, but mutations were also observed in signaling genes (25% of the patients). Thirty eight percent of the alterations lost at relapse (“Loss” and “Gain and Loss” patterns) are found in signaling genes (i.e FLT3, KIT, KRAS, NRAS ) and 23% in myeloid transcription factors (i.e CEBPA, RUNX1, GATA2 ). It was also been observed that 47% of mutations thatwere observed in each group at diagnosis and relapse were localized in DNA methylation and chromatin modification genes (i.e DNMT3A, IDH1/2, TET2, ASXL1, EZH2 ).Interestingly, at diagnosis, mutations of DNA methylation and spliceosome complex genes were preferentially observed in the “Gain” pattern group (p=0.040). In contrast, mutations of signaling genes were preferentially mutated at diagnosis in the “Loss” group (p=0.020).Even if not statistically significant, we observed that evolution and prognosis seemed to be different among the different patterns. The “Gain” pattern tends to have shorter overall survival (median 14.7 months vs 22.9 months in Stability group) whereas in the “Loss” group, overall survival appeared longer (median 34.1 months). Moreover, patients in the “Gain” group were significantly older (p=0.017), and were classified as AML with myelodysplasia-related changes in most of the cases.To our knowledge, our work is the first reporting multiplex targeted NGS sequencing in AML at diagnosis and relapse. The comparison of clonal landscape between diagnosis and relapse allowed us to define 5 evolution patterns that differed in terms of mutation landscape and evolution.Even if these data must be confirmed on a larger cohort, our study shows the feasibility of clonal analysis using targeted NGS at diagnosis and relapse in AML and its potential prognosis interest in clinical routine. DisclosuresNo relevant conflicts of interest to declare.

Experimental Models of Liquid Biopsy in Hepatocellular Carcinoma Reveal Clone-Dependent Release of Circulating Tumor DNA.

Liquid biopsy, the molecular analysis of tumor components released into the bloodstream, has emerged as a noninvasive and resourceful means to access genomic information from cancers. Most data derived from translational studies showcase its numerous potential clinical applications. However, data from experimental models are scarce, and little is known about the underlying mechanisms and factors controlling the release of circulating tumor DNA (ctDNA) and cells (CTCs). This study aimed to model liquid biopsy in hepatocellular carcinoma xenografts and to study the dynamics of release of ctDNA and CTCs; this included models of intratumoral heterogeneity (ITH) and metastatic disease. We quantified ctDNA by quantitative polymerase chain reaction (PCR) targeting human long interspersed nuclear element group 1; targeted mutation analysis was performed with digital droplet PCR. CTCs were traced by flow cytometry. Results demonstrated the feasibility of detecting ctDNA, including clone‐specific mutations, as well as CTCs in blood samples of mice. In addition, the concentration of ctDNA and presence of tumor‐specific mutations reflected tumor progression, and detection of CTCs was associated with metastases. Our ITH model suggested differences in the release of DNA fragments impacted by the cell‐clone origin and the treatment. Conclusion: These data present new models to study liquid biopsy and its underlying mechanisms and highlighted a clone‐dependent release of ctDNA into the bloodstream.

Frequency and Distribution of MEFV Gene Mutation in Familial Mediterranean Fever Patients: A Single Center Experience

Objective We aimed to evaluate frequency and distribution MEFV gene mutation variants in patients with presumptive diagnosis of Familial Mediterranean Fever (FMF). Material and Methods Patients who had undergone FMF targeted mutation analysis between September 2018 and September 2019 were retrospectively analyzed. Twenty-six distinct MEFV gene mutation variants were studied. Demographic and clinical data of study participants were collected from patient charts and hospital electronic database system. Results Out of 910 referred patients, 350 (38.5%) were found to have a positive FMF mutation. In total, we detected 41 different genotypes and 26 different mutations in MEFV gene. The most common mutation and genotype were M694V and heterozygous M694V, respectively. Two hundred and seventy-six patients (78.9%) had a single mutation. Seventy-four patients had compound heterozygous mutation (21.1%). The most common compound heterozygous mutation was P369S/R408Q (23.3%). Five founder mutations constituted the seventy-five percent of the all mutations detected. Rare mutations that generally not examined in other studies were present in 15 patients (%4.2) in the form of two different compound heterozygous genotype. The total allele frequency of these rare mutations was 5%. Conclusion In this study, we examined an extended panel of MEFV mutations and detected more complex genotypes than most of the previous studies conducted in Turkish patients in the literature.

NCOG-38. CLINICAL CHARACTERISTICS OF LOW GRADE GLIOMA PATIENTS WITH NON-CANONICAL IDH1 AND IDH2 MUTATIONS

Abstract BACKGROUND Low grade gliomas (LGGs) develop in young adults and represent 10-15% of all glial tumors. While LGG patients can have longer survival than higher grade tumors, progression, transformation, and ultimately mortality occurs. Mutations in Isocitrate dehydrogenase 1/2 (IDH1/IDH2) are prevalent in LGG and are responsible for gliomagenesis. The classic IDH1 mutation is located at 132 codon and represented as p.Arg132His, but there are non-canonical IDH1 and IDH2 mutations. We sought to compare clinical characteristics of LGG patients with classic IDH1 p.Arg132His mutation to LGG patients with non-canonical IDH1 and IDH2 mutations. METHODS We queried an IRB-approved registry retrospectively from 12/2004- 9/2019. We included IDH1/IDH2 mutant LGG (WHO grade II) and known IDH1 and IDH2 targeted mutation analysis using standard PCR followed by DNA sequencing to detect point mutations in IDH1/IDH2 genes. We obtained available clinical and histopathological data. We estimated progression-free survival (PFS), time to transformation (TT), and overall survival (OS) using Kaplan-Meier methods. RESULTS We identified 267 LGG patients with median follow-up of 9.1 yrs (95%CI 8.4-9.9 yrs). Classic IDH1 p.Arg132His mutation occurred in 223 (83.9%) patients. IDH2 mutations occurred in 14 (5.2%) patients. Non-canonical IDH1 mutations were in 30 (11.2%) patients and included the following mutations: p.Arg132Cys (13), p.Arg132Gly (10), p.Arg132Ser (4), p.Arg132Leu (1), p.Arg119Gln (1), and p.Arg172Met (1). Initial presentation, OS, and TT did not differ between IDH1/IDH2 groups. PFS differed significantly between groups with improved median PFS in IDH2 mutant LGG (5.4 yrs; 95%CI 3.5-25.2) versus classic IDH1 mutant LGG (4.1 yrs; 95%CI 3.7-4.9 yrs) and non-canonical IDH1 mutant LGG (2.6 yrs; 95%CI 2.1-4.8) (log-rank p=0.019). Notably, non-canonical mutations were more common in astrocytoma (22/30; 73.3%) than other LGG histologies (p=0.018). CONCLUSIONS In this cohort, LGG patients with non-canonical mutations have a shorter time to progression than patients with classic p.Arg132His mutation and IDH2 mutations.

The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma

Intraductal papillomas (IDP) are challenging breast findings because of their variable risk of progression to malignancy. The molecular events driving IDP development and genomic features of malignant progression are poorly understood. In this study, genome-wide CNA and/or targeted mutation analysis was performed on 44 cases of IDP, of which 20 cases had coexisting ductal carcinoma in situ (DCIS), papillary DCIS or invasive ductal carcinoma (IDC). CNA were rare in pure IDP, but 69% carried an activating PIK3CA mutation. Among the synchronous IDP cases, 55% (11/20) were clonally related to the synchronous DCIS and/or IDC, only one of which had papillary histology. In contrast to pure IDP, PIK3CA mutations were absent from clonal cases. CNAs in any of chromosomes 1, 16 or 11 were significantly enriched in clonal IDP lesions compared to pure and non-clonal IDP. The observation that 55% of IDP are clonal to DCIS/IDC indicates that IDP can be a direct precursor for breast carcinoma, not limited to the papillary type. The absence of PIK3CA mutations and presence of CNAs in IDP could be used clinically to identify patients at high risk of progression to carcinoma.

Spectrum of germline BRCA mutations in hereditary breast and ovarian cancer syndrome in Indian population: A central reference laboratory experience

Introduction: There is a growing need for BRCA1/BRCA2 mutation frequencies among hereditary breast and ovarian carcinoma (HBOC) cases, specifically determined on the grounds of personal and family history profiles in the Indian population. The current study was intended to identify BRCA1/2 mutation frequency and spectrum in Indian women fulfilling the National Comprehensive Cancer Network criteria.Methods: One hundred and sixty unrelated women were screened for germline variations in BRCA1 and BRCA2 genes by sequencing. The variants were classified as pathogenic or benign on the basis of American College of Medical Genetics (ACMG) guidelines.Results: Of 160 women screened for BRCA mutations, 51 (31.9%) carried a pathogenic variant in BRCA1 (n = 36) or BRCA2 (n = 15) gene. An increased frequency of mutation was seen in women with a personal history of breast or ovarian cancer (34.5%) in comparison to unaffected family members (25%). A spectrum of 34 different pathogenic variants (20 in BRCA1 and 14 in BRCA2) was identified in 51 cases. This included a novel variant c.3683_3684dup in BRCA1 which was categorized as a pathogenic variant. The variant c.68_69delAG in BRCA1 was identified in 12/51 positive cases and appears to be the hotspot mutation in the Indian population. In addition, 11 different missense variants were identified in 10 of the study participants and were categorized as variants of unknown clinical significance (VUS) based on the ACMG guidelines. Of these, three of the variants (c.389A>C in BRCA1 and c.3179G>A and c.10124G>T in BRCA2) were unreported in the published literature.Conclusion: The prevalence of pathogenic variants in the Indian HBOC cohort is high and is similar to other Indian studies. The spectrum of BRCA variants is also diverse, and it is very important to correctly classify them as pathogenic, VUS, or benign. We reinforce the importance of complete BRCA gene screening in the index case, followed by genetic counseling and targeted mutation analysis in other at-risk family members.

Profiling of Circulating Free DNA Using Targeted and Genome-wide Sequencing in Patients with SCLC

IntroductionSCLC accounts for approximately 250,000 deaths worldwide each year. Acquisition of adequate tumor biopsy samples is challenging, and liquid biopsies present an alternative option for patient stratification and response monitoring.MethodsWe applied whole genome next-generation sequencing to circulating free DNA (cfDNA) from 39 patients with limited-stage (LS) SCLC and 30 patients with extensive-stage SCLC to establish genome-wide copy number aberrations and also performed targeted mutation analysis of 110 SCLC associated genes. Quantitative metrics were calculated for copy number aberrations, including percent genome amplified (PGA [the percentage of genomic regions amplified]), Z-score (a measure of standard deviation), and Moran’s I (a measure of spatial autocorrelation). In addition CellSearch, an epitope-dependent enrichment platform, was used to enumerate circulating tumor cells (CTCs) from a parallel blood sample.ResultsGenome-wide and targeted cfDNA sequencing data identified tumor-related changes in 94% of patients with LS SCLC and 100% of patients with extensive-stage SCLC. Parallel analysis of CTCs based on at least 1 CTC/7.5 mL of blood increased tumor detection frequencies to 95% for LS SCLC. Both CTC counts and cfDNA readouts correlated with disease stage and overall survival.ConclusionsWe demonstrate that a simple cfDNA genome-wide copy number approach provides an effective means of monitoring patients through treatment and show that targeted cfDNA sequencing identifies potential therapeutic targets in more than 50% of patients. We are now incorporating this approach into additional studies and trials of targeted therapies.

Mutations of RAS genes in endometrial polyps.

Endometrial polyps are common, yet the molecular mechanisms underlying their formation and progression remain unclear. We examined gene mutations possibly related to the pathogenesis of endometrial polyps, as well as to their clinical features. Four premenopausal patients with endometrial polyps, who were not under drug treatment, were recruited. Whole exomes of endometrial polyps and peripheral blood lymphocytes were analyzed by next-generation sequencing, and somatic mutations were derived by subtraction. Then, 35 samples of endometrial polyps and 12 samples of atypical polypoid adenomyoma were newly recruited to validate the identified mutations by polymerase chain reaction-reverse sequence specific oligonucleotide method. The mutations were also analyzed in separate stromal and glandular components of the polyps after laser-capture microdissection. Whole exome sequencing revealed that KRAS mutations were the only type of mutation detectable in multiple cases (2/4). Targeted mutation analysis revealed that 16 of 35 samples (45.7%) of endometrial polyps harbored RAS mutations. Mutation-positive cases exhibited a significantly higher number of endometrial polyps (3.25±2.70 vs. 1.74±0.87, P=0.045). Laser-capture microdissection in NRAS-mutated endometrial polyps revealed that both stromal and glandular components harbored RAS mutations. There was no RAS mutation in 12 samples of atypical polypoid adenomyoma. This is the first report demonstrating that pathogenic RAS mutations are frequent in non-treated endometrial polyps. RAS mutations may have an important role in tumorigenesis and in the formation of multiple endometrial polyps.

Prenatal Diagnosis of Organic Acidemias at a Tertiary Center.

The aim of this study was to share our experience in the prenatal diagnosis (PND) of organic acidemias (OAs) in our clinic. This study consisted of 10 cases in whom an invasive prenatal diagnostic test (IPNDT) was performed by a single physician for the PND of OAs. Median maternal age, parity, gestational week of IPNDT, prenatal test indications, OA types, method of IPNDT, IPNDT results and gestational outcomes were evaluated. Targeted mutation analysis was performed in fetal DNA for the specific mutations by using polymerase chain reaction (PCR) and direct Sanger sequencing. The diagnosis was confirmed by genetic targeted mutation analysis after birth. Median maternal age, parity and gestational week of IPNDT values were 30 (range 21-35), one (range 0-4) and 11.5 (range 11-17), respectively. Indications for IPNDT were mother being a carrier of the disease for one case (10.0%) and at least one child with OA in the family for nine cases (90.0%). Organic acidemia types investigated were maple syrup urine disease (MSUD), methylmalonic acidemia (MMA) and isovaleric acidemia (IVA) in five (50.0%), three (30.0%) and two (20.0%) patients, respectively. Chorion villus sampling (CVS) was done in seven (70.0%) patients and amniocentesis was performed in three (30.0%) patients. Eight fetuses (80.0%) were found to be healthy and two fetuses (20.0%) were found to be affected (one case with IVA and one case with MMA). The two pregnancies (20.0%) with affected fetuses were terminated. Prenatal diagnosis of OAs is critical. Appropriate prenatal counseling should be given to families with known risk factors.

IDH1 immunohistochemistry reactivity and mosaic IDH1 or IDH2 somatic mutations in pediatric sporadic enchondroma and enchondromatosis.

Mosaic somatic mutations in the isocitrate dehydrogenase 1/2 (IDH1/2) genes have been identified in most enchondromas by targeted mutation analysis. Next-generation sequencing (NGS), that may detect even low-level mosaic mutation rates, has not previously been applied to enchondromas. Immunohistochemistry using the H09 clone is routinely used as a surrogate for the common R132H IDH1 mutation in gliomas. We compared immunohistochemistry and NGS results in a series of 13 enchondromas from 8 pediatric patients. NGS identified a heterozygous IDH mutation in all enchondromas, showing identical mutation status in patients with multiple tumors assessed, thereby confirming somatic mosaicism. A majority of the tumors harbored an IDH1 mutation (p.R132H in 3 tumors; p.R132C in 4 tumors from 2 patients; p.R132L and p.R132G in one tumor each). A p.R172S IDH2 mutation was identified in 4 enchondromas, but not in the ependymoma from one patient with Ollier disease, who further displayed a heterozygous STK11 missense mutation. IDH mutation rates varied between 14% (indicative of mutations in 28% of the cells and of intratumoral mosaicism) and 45% (tumor content was close to 100%). Cytoplasmic H09 reactivity was observed as expected in tumors with an IDH1 p.R132H mutation; cross-reactivity was seen with the p.R132L variant. This first NGS study of pediatric enchondromas confirms that IDH mutations may occur in a mosaic fashion. STK11 gene mutations may provide insights in the development of multiple cartilaginous tumors in enchondromatosis, this tumor suppressor gene having been shown in animal models to regulate both chondrocyte maturation and growth plate organization during development.

Myasthenic congenital myopathy from recessive mutations at a single residue in NaV1.4.

ObjectiveTo identify the genetic and physiologic basis for recessive myasthenic congenital myopathy in 2 families, suggestive of a channelopathy involving the sodium channel gene, SCN4A.MethodsA combination of whole exome sequencing and targeted mutation analysis, followed by voltage-clamp studies of mutant sodium channels expressed in fibroblasts (HEK cells) and Xenopus oocytes.ResultsMissense mutations of the same residue in the skeletal muscle sodium channel, R1460 of NaV1.4, were identified in a family and a single patient of Finnish origin (p.R1460Q) and a proband in the United States (p.R1460W). Congenital hypotonia, breathing difficulties, bulbar weakness, and fatigability had recessive inheritance (homozygous p.R1460W or compound heterozygous p.R1460Q and p.R1059X), whereas carriers were either asymptomatic (p.R1460W) or had myotonia (p.R1460Q). Sodium currents conducted by mutant channels showed unusual mixed defects with both loss-of-function (reduced amplitude, hyperpolarized shift of inactivation) and gain-of-function (slower entry and faster recovery from inactivation) changes.ConclusionsNovel mutations in families with myasthenic congenital myopathy have been identified at p.R1460 of the sodium channel. Recessive inheritance, with experimentally established loss-of-function, is a consistent feature of sodium channel based myasthenia, whereas the mixed gain of function for p.R1460 may also cause susceptibility to myotonia.

Targeted Mutation Analysis of the SLC26A4, MYO6, PJVK and CDH23 Genes in Iranian Patients with AR Nonsyndromic Hearing Loss

Background: Hearing loss (HL) is the most prevalent sensory disorder. The over 100 genes implicated in autosomal recessive nonsyndromic hearing loss (ARNSHL) makes it difficult to analyze and determine the accurate genetic causes of hearing loss. We sought to de?ne the frequency of seven hearing loss-Causing causing genetic Variants in four genes in an Iranian population with hearing loss. Materials and methods: One hundred ARNSHL patients with normal GJB2/GJB6 genes were included, and targeted mutations in SLC26A4, MYO6, PJVK and CDH23 genes were analyzed by ARMS-PCR. The negative and positive results were confirmed by the Sanger sequencing. Results: We found only two mutations, one in MYO6 (c.554-1 G > A) gene and another in PJVK (c.547C > T). Conclusion: c.554-1G > A and c.547C > T mutations are responsible for 1% each of the Iranian ARNSHL patients. These genes are not a frequent cause of ARNSHL in an Iranian population.