Evaluation of Single Exon Deletions in DMD/BMD: Technical and Analytical Concerns.

Background: Oftentimes, a variation at the multiplex ligation-dependent probe amplification (MLPA) probe binding site leads to improper hybridrization/ligation of the probe showing up as a deletion of an exon leading to false positive results for the detection of Duchenne muscular dystrophy (DMD)/Becker muscular dystrophy (BMD). Objective: Investigating cases with single exon deletion using an alternate method [polymerase chain reaction (PCR) or sequencing] for confirmation of the deletion. Methods: We evaluated males with single exon deletion (n = 49) in our study population (2015-2019). Forty-six were confirmed by an alternate method (conventional PCR/Sanger's sequencing) to confirm the deletion. Results: We observed 25.12% single exon deletions in our study cohort. Further evaluation determined a false positive rate of 6.12%. Three out of 49 single exon deletions had a point mutation near the probe-binding site, indicating a false positive result. Single exon deletions, thus, need to be evaluated with extreme caution, and point mutations, if any, need to be characterized to determine the nature of their pathogenicity.

Next generation sequencing in lung cancer: An initial experience from India.

INTRODUCTION: Approximately 35% of NSCLC patients in East Asia have EGFR mutations. Next-generation sequencing (NGS) provides a comprehensive mutational profile in lung cancer patients. MATERIAL AND METHOD: Clinicopathologic characteristics and mutational profiling data was analyzed from nonsmall cell lung carcinoma /Adenocarcinoma over a duration of 42 months (October 2014 to March 2018) using next-generation sequencing Ion Ampliseq Cancer Hotspot panel v2 (Ampliseq, Life Technologies) on the Ion torrent PGM platform. RESULTS: A total of 154 cases were processed during this period. The average number of mutations/case varied from one to four 72.07% (111/154), of these cases had minimum one genetic alteration. The most common mutated gene was TP53 gene (37.6%, n = 58) followed by EGFR (32.4%, n = 50), KRAS (18.18%, n = 28), ERBB2 (3.2%, n = 5), BRAF (1.94%, n = 3). EGFR positivity was more in females (43.3%) and non-smokers (52.08%) in comparison to males (26.7%) and smokers (16.1%). CONCLUSION: In this paper, we have described the comprehensive mutational profiling of a large cohort of advanced lung adenocarcinoma patients from the eastern part of India. To the best of our knowledge, this is one of the largest studies from the country describing mutations in BRAF, ERBB2, TP53 genes and their clinicopathologic/histopathologic associations in lung cancers.

MYD88 and CXCR4 Mutation Profiling in Lymphoplasmacytic Lymphoma/Waldenstrom's Macroglobulinaemia.

Recurrent mutations affecting MYD88 and CXCR4 gene nowadays form the basis for the diagnosis, risk stratification and use of inhibitors targeting these signalling pathways in LPL/WM which are rare B cell neoplasms. MYD88 L265P mutation analysis was performed on 33 cases of LPL/WM by AS-PCR (positivity-84.8%, n = 28/33) and by Sanger sequencing (positivity-39.3%, n = 13/33). We had only two cases with CXCR4 non-sense (NS) mutation (p.S338*) using Sanger sequencing. MYD88 (L265P) mutation detection by AS-PCR can form reliable biomarker for the diagnosis of LPL/WM in molecular labs. Although the cohort is small, still the CXCR4 mutation frequency in our study is low as compared to the published literature.

A novel CFTR gene variant - p.Tyr517* associated with cystic fibrosis: a case report.

INTRODUCTION: Cystic fibrosis (CF) is a genetic disease usually diagnosed by clinical findings and abnormal sweat chloride testing. CASE REPORT: We report a case of an 18-month-old Indian female with clinical findings suggestive of CF referred for genetic confirmation. The CFTR gene was sequenced for 23 mutations as per American College of Medical Genetics (ACMG) guidelines for CF and showed presence of a known common heterozygous delF508 (c.1521_1523delCTT, p.Phe508 del) variant. In addition to delF508 variant, exon 10 of CFTR gene also showed a novel variant c.1551C > G, p.Tyr517*, which was classified as "likely pathogenic" based on recent ACMG variant classification guidelines. The presence of compound heterozygous pathogenic variants along with classical clinical findings, confirmed the diagnosis of CF in this patient. CONCLUSION: The novel pathogenic variants (missense/nonsense/deletion/duplication) in CFTR gene are often identified and are associated with CF, thus highlighting the need of comprehensive complete CFTR gene analysis.

Small cell medullary thyroid carcinoma: A diagnostic dilemma.

Small cell variant of medullary thyroid carcinoma (MTC) is a rare variant. In the past, primary thyroid lymphomas were thought to be small cell MTC (SCMTC). However, with the advent of immunohistochemistry, it was realized that SCMTC is rare. Our patient presented with neck mass for 1 year with an outside laboratory report of neoplastic lesion. His serum calcitonin levels were normal, but serum carcinoembryonic antigen (CEA) levels were high. He underwent total thyroidectomy and was diagnosed to have small cell variant of MTC. Immunohistochemistry for AE1/AE3 and CEA were positive while calcitonin was negative. The patient underwent radiotherapy but developed metastasis 3 months later. Thus, SCMTC is a rare and aggressive variant of MTC. In the absence of raised serum calcitonin levels, raised serum CEA levels are helpful. It is necessary to identify this rare variant as it connotes a poor prognosis and should be treated aggressively.