Atypical Co-amplification with Co-localization of HER2 Gene in Breast Cancer: Combined IHC/FISH Approach as per ASCO/CAP 2018 Guidelines for Targeted Therapy Eligibility.

Breast cancer patients with HER2 gene amplification as assessed by FISH are eligible for HER2-targeted therapy. However, in a small subset of patients, unusual FISH pattern of co-localization and co-amplification can pose challenges in interpretation of the HER2 status and hence to assess the HER2 status accurately; our aim was to report their incidence and analyze them based on latest ASCO/CAP 2018 guidelines. We present seven cases with HER2/CEP17 co-amplification and co-localization from a total 4040 cases referred during the year 2017 to 2021 at Mumbai Reference Laboratory, SRL Diagnostics. Core needle biopsy/excision invasive breast carcinoma specimens from metastatic sites were tested for IHC for expressions of ER, PR, and HER2. The ones which came equivocal on HER2 IHC were then evaluated for HER2 amplification by FISH. Co-amplification and co-localization of HER2 and centromeric 17 was observed with a frequency of 0.1% that falls in the range of 0.5-0.1% as reported from other large-scale studies. Our study showed that implementation of a binary inhouse concurrent assessment with IHC as per the ASCO/CAP 2018 helps to reach the most definitive and accurate HER2 status. Our study is an attempt to report such challenging FISH patterns and their work-up for a better understanding on the interpretation. Cumulative data along with follow-up in these cases would bring an insight into exact therapeutic outcome.

Derivative 6 as an additional chromosomal abnormality along with t(15;17): A case report.

Acute promyelocytic leukemia (APL) is a type of acute myeloid leukemia (AML) characterized by the presence of t(15;17)(q22;q21) translocation leading to fusion between PML and RARa gene. Treatment combining all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) has dramatically improved the prognosis of APL. We report a rare finding of primary clone of t(15;17) followed by a sequential clonal evolution of additional derivative chromosome 6 formation by a two hit mechanism. Our case showed a good clinical response with a four years and nine months event free survival after ATRA and ATO combination therapy in spite of existence of three chromosomal abnormalities stating that targeted therapy overcomes the adverse effects of additional genetic markers. However, close monitoring with assessment for long term prognostic behavior is required.

A novel coexistence of tetrasomy 8 and FLT3-ITD along with variant 3 way translocation t(4;17;15) in acute promyelocytic leukemia: Case study and literature review.

Here, we report a case of Acute promyelocytic leukemia (APL) with three way complex translocation involving chromosomes 4, 15, and 17. Although chromosome 4 is most commonly associated chromosome in three way translocation, present case is the first report with four novel co-existent findings of new break point region on chromosome 4, new cyclic mechanism with simultaneous breaks, presence of a co-existent tetrasomy 8 and FLT3 ITD positivity.; Comprehensive assessment highlight the utility of combining morphology, immunophenotyping, karyotyping, fluorescence in situ hybridization, and molecular studies for better characterization, optimal management of APL with a better understanding of the pathogenic mechanism and prognosis of the disease.

Atypical MYC rearrangement pattern of 3' deletion and 5' amplification along with independent IGH rearrangement: A case study.

A spectrum of Cellular homolog of the v-myc oncogene (cMYC) alterations such as translocation, overexpression, mutation, and amplification plays an important role in lymphomagenesis, particularly in high-grade lymphomas, and are associated with prognostic significance. Accurate identification of cMYC gene alteration is important for diagnostic, prognostic, and therapeutic implications. With the application of different FISH (fluorescence in situ hybridization) probes that helped overcome the analytical diagnostic challenges as a result of variant patterns, we report rare, concomitant, and independent gene alterations in cMYC and Immunoglobulin heavy-chain gene (IGH) with detailed characterization of its variant rearrangement. Short-term follow-up post R-CHOP (rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone) therapy seemed to be favorable. Accumulation of many more literature studies on such cases with their therapeutic implications would lead to the categorization of these cases as a separate subclass in large B-cell lymphomas followed by molecular targeted therapy.

A complex karyotype with t(11;12)(q23;p13) translocation with coexistent clones of deletion 5q and cryptic deletion 7q in acute myeloid leukemia.

We report a rare case of acute myeloid leukemia (AML) with a cytogenetically complex karyotype with coexistence of KMT2A/MLL Mixed Lineage Leukemia (11q23) rearrangement with 5q deletion and 7q deletion as unrelated clones along with evolution of a subclone with translocation between chromosomes 6 and 17. A novel MLL fusion partner region 12p13 was identified in a 52 year old woman who presented with pyrexia of unknown origin. Unraveling the complexity of genomic alterations occurring in AML patients will lead to better understanding of leukemic transformation and identification of subsets of patients that may respond differently to therapy.

A Study of Triplet-Primed PCR for Identification of CAG Repeat Expansion in the HTT Gene in a Cohort of 503 Indian Cases with Huntington's Disease Symptoms.

BACKGROUND: Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder with an average age at onset of 40 years. It is a polyglutamine (polyQ) disorder that is caused by an increase in the number of CAG repeats in the huntingtin (HTT) gene. Genetic tests that accurately determine the number of CAG repeats are performed for confirmation of diagnosis, predictive testing of persons at genetic risk for inheriting HD, and prenatal testing. The aim of our study was to evaluate efficacy of triplet-primed polymerase chain reaction (TP-PCR) for routine diagnosis of HD in suspected cases from India. METHODS: We evaluated a combination of CAG flanking PCR and triplet-primed PCR for estimation of CAG repeats in 503 cases with clinical suspicion of HD. RESULTS: There were 250 cases (49.7%) that showed the presence of expanded alleles, with 241 (47.9%) being fully penetrant alleles and nine (1.8%) in the reduced penetrance category. There were seven juvenile cases with an age of onset of < 20 years, with the longest allele comprising 106 CAG repeats found in an 8-year-old male patient. The results demonstrated an inverse (R = - 0.67) relationship between CAG length and age at clinical onset. CONCLUSION: Our study on pan-Indian cases is one of the largest studies reported so far in India and focuses on the most accurate and comprehensive molecular diagnostic evaluation of HD.

Spectrum of cytomorphological features, including literature review, of an extraskeletal myxoid chondrosarcoma with t(9;22)(q22;q12) (TEC/EWS) results in one case.

Extraskeletal myxoid chondrosarcoma (EMC) is an uncommon soft tissue sarcoma with evolving literature on its cytomorphological features and limited documentation of its molecular analysis. Herein, we present cytological features, including review, of four cases of an EMC. Smears were predominantly hypercellular, comprising tumor cells arranged in clusters, traberculae, and cords against a variable chondromyxoid background. Cells were mainly polygonal shaped with round to indented nuclei, uniform chromatin, displaying intranuclear inclusions, grooves, and eosinophilic to finely vacuolated cytoplasm. Three cases revealed presence of "rhabdoid" cells. All cases had histopathologic confirmation. One case displayed t(9;22)(q22;q12) translocation by fluorescent in situ hybridization (FISH), on smears.

RUNX1 aberrations in ETV6/RUNX1-positive and ETV6/RUNX1-negative patients: its hemato-pathological and prognostic significance in a large cohort (619 cases) of ALL.

A large-cohort study (619) of acute lymphoblastic leukemia (ALL) revealed an ETV6/RUNX1 (previously known as TEL/AML1) incidence of 18% in pediatric B-cell precussor ALL, indicating no geographical heterogeinity. Association of CD34-negative phenotype, peak incidence in the 3- to 7-year age group, and a comparatively low frequency of ETV6 homologue loss in ETV6/RUNX1-positive cases were distinct findings in this series. Additional genetic changes, such as ETV6 loss, extra RUNX1, ETV6/RUNX1 duplication, and MLL aberrations in the ETV6/RUNX1-positive group, supported the hypothesis of the ETV6/RUNX1 leukemogenic model that these secondary changes are necessary for leukemogenesis rather than progression of disease. This study disclosed RUNX1 alterations in the ETV6/RUNX1-negative group of BCP-ALL that encourages the investigation of RUNX1 at a large scale with longer follow-up, which will focus on the prognostic importance and the underlying biology of disease.

Coexistence of ETV6/RUNX1 and MLL aberrations in B-cell precursor acute lymphoblastic leukemia discloses a small subclass of BCP-ALL.

Out of 76 pediatric cases of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) positive for ETV6/RUNX1 (previously TEL/AML1) resulting from t(12;21), 7 cases revealed coexistence of ETV6/RUNX1 and MLL aberrations. One case of der(21) duplication with ETV6/RUNX1 exhibited a novel MLL translocation variant t(6;11)(p21.1p23;q13q25), with translocation of 3' telomeric MLL and deletion of 5' centromeric MLL. Another case of der(21) duplication with ETV6/RUNX1 showed MLL rearrangement upon Southern blotting. The remaining five ETV6/RUNX1-positive cases had MLL allelic deletion. ETV6/RUNX1 and MLL aberration clone size in these cases was suggestive of ETV6/RUNX1 as an early primary event, originating in the embryonic or infant stage and developing into leukemia by later acquisition of MLL aberration, ETV6 loss, and ETV6/RUNX1 duplication as secondary events. To date, the prognosis has been favorable, which seems to be compatible with ETV6/RUNX1-positive ALL. We conclude that the cases with coexisting ETV6/RUNX1 and MLL aberrations probably exist as a small, hidden group of ETV6/RUNX1-positive BCP-ALL, which invites further investigation, in large series from different populations, to confirm the findings and establish the biological mechanisms and prognostic significance.

Identification of various MLL gene aberrations that lead to MLL gene mutation in patients with acute lymphoblastic leukemia (ALL) and infants with acute leukemia.

Studies were done to investigate MLL gene aberrations using Conventional Cytogenetics, Southern blotting as well as FISH using a panel of probes on 218 cases which included 206 cases of pediatric/young adult ALL and 12 cases of infantile acute leukemias from Tata Memorial Hospital, India. The incidence of MLL gene rearrangements in acute lymphoblastic leukemia (ALL) was 9.4% which included infants as well as pediatric/young adults. In infantile group which included ALL as well as AML cases, MLL gene rearrangement was very common (75% frequency). Application of metaphase-FISH helped unravel MLL rearrangements not only as a result of translocations but also inversions, insertions, partial deletion, duplications, partial duplication-->self-fusion. Besides age, MLL gene rearrangements showed significant association with hyperleukocytosis, peripheral blood blast percentage and early Pre-B phenotype. Clinical outcome of patients with MLL gene rearrangements revealed unfavorable prognosis.