Test Your Knowledge

Correct answer: A

Explanation of answer:  MEN1 encodes a nuclear scaffold protein, menin, which is involved in regulating gene expression and genomic integrity (PMID:23850066). Pathogenic germline variants in MEN1 are associated with multiple endocrine neoplasia type 1 (MEN1), a autosomal dominant condition features with parathyroid tumor, gastroenteropancreatic neuroendocrine tumor, and anterior pituitary tumor (PMID:22723327, 20301710).

Correct answer: B

Explanation of answer: NCCN guidelines v2 2024 (November 1, 2023): del(17p) and/or translocation t(4;14) and/or translocation t(14;16) are considered as high risk in patients with multiple myeloma (MM). 

Deletion, and NOT a gain, of 1p32 is among typical findings in MM; t(11;14) is associated with an intermediate risk for survival time; trisomy 8 carries poor prognosis in patients with acute myeloid leukemia but is a rare finding in patients with MM.
 

Correct answer: D

Explanation of answer: Glioblastoma is the most frequent malignant brain tumour in adults, accounting for approximately 15% of all intracranial neoplasms. In children, it accounts for approximately 3% of all CNS tumours. Glioblastoma, IDH-wildtype, is a diffuse, astrocytic glioma that is IDH-wildtype and H3-wildtype and has one or more of the following histological or genetic features: microvascular proliferation, necrosis, TERT promoter mutation, EGFR gene amplification, combined +7/−10 chromosome copy-number changes (CNS WHO grade 4).

Correct answer: C

Explanation of answer: Proportion of PWS attributed by mechanism: 15q deletion (60-70%), UP15 complete isodisomy (4-5%), UPD15 segmental isodisomy (17-23%), UPD15 heterodisomy (8-11%), Imprinting center deletion (<0.5%), ICR epimutation (2-4%).

Correct answer: B

Explanation of answer: Germline pathogenic changes in PHOX2B are associated with autosomal dominant Congenital Central Hypoventilation Syndrome (CCHS). It was reported to have increased risk for Hirschsprung disease and neuroblastoma (PMID: 15657873, 20301600). Clinical presentation varies due to variable expressivity, reduced penetrance, and somatic mosaicism (PMID: 16888290, 27485184)

Correct answer: D

Explanation of answer: The pedigree shows a mitochondrial maternal inheritance pattern, where the females in the family pass the disorder to the next generation, but the male in generation II cannot pass it to the next generation.

Correct answer: B

Explanation of answer: Oligodendrogliomas are molecularly defined by IDH1 or IDH2 mutations and 1p/19q codeletion, and only complete whole arm losses of both chromosome arms are diagnostic for oligodendroglioma (Louis DN, et al. The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol. 2021 Aug 2;23(8):1231-1251. PMID: 34185076) 

Correct answer: D

Explanation of answer: All the others (HCL, Melanoma, CRC) recurrently demonstrate BRAF V600E. Lymphoplasmic lymphoma is associated with MYD88 mutations, specifically L265P.

Correct answer: A

Explanation of answer: Methylation analysis on brain tumors has proven to be an accurate diagnostic tool.

Correct answer: C

Explanation of answer: The most common mechanism for inherited cancer predisposition is a pathogenic germline variant and then an acquired second hit on the wild type allele.

Correct answer: A

Explanation of answer: While FISH, CMA, and sometimes karyotype (depending on resolution) can indicate a deletion in the region of PWS, only methylation sensitive PCR can identify which parental allele that the deletion resides on

Correct answer: B

Explanation of answer: The cycle-threshold is defined as the fractional cycle number in the log-linear region of PCR amplification in which the reaction reaches fixed amounts of amplicon DNA.

Correct answer: D

Explanation of answer: Balanced translocations are a common finding in normal phenotype parents with recurrent pregnancy loss.

Correct answer: B

Explanation of answer: Knowing the reason for referral is important for cell culture selection.

Correct answer: C

Explanation of answer: When multiple probes demonstrate copy gains, the most likely answer is a hyperdiploid karyotype; however, it is important to demonstrate this subtype by either multiple centromere probes (FISH) or by karyotype. 

Correct answer: B

Explanation of answer: This is a question about how to read the ISCN properly. Because there is no indication of acknowledgment of a stemline in the second set of cells, this indicates that there are two separate abnormal populations of cells comprising a total of 40% of the cells. The remaining 12 (60%) are normal. While one may expect to see the clones as related in disease, it is possible the two lines either appeared separately or they may represent subclones in the main disease line with another genetic driver (e.g. SF3B1 as the driver with one subclone with del(5q) and the other subclone +8). Using just the karyotype, one cannot differentiate between these two possibilities. 

Correct answer:  B

Explanation of answer: Amplification of MDM2, CDK4 can be useful to distinguish Atypical lipomatous tumor/well-differentiated liposarcoma and Dedifferentiated liposarcoma from benign tumors. These amplifications are generally detected as supernumerary rings and giant marker chromosomes on karyotype.

Correct answer: D

CEBPA-mutated acute myeloid leukemia (AML) is its own diagnostic category within the WHO Classification of Haematolymphoid Tumors. Current literature supports the presence of CEBPA biallelic mutations (i.e., biCEBPA) or single mutations located within the 3' basic leucine zipper (bZIP) region of the gene (i.e., smbZIPCEBPA) as favorable, whereas single mutations found outside of this bZIP region do not have a more favorable prognosis (as compared with CEBPA-wildtype AML). Thus, answer A would not be correct. N-terminal CEBPA mutations have been shown to occur in the germline of individuals with AML at a higher frequency than variants located within other regions of the gene. Although in a tumor-only test setting the location of this variant in the N-terminus of CEBPA would support further investigation into the origin of this variant, the paired tumor/normal design of the NGS assay confirms that this N-terminal variant is somatic. Thus, answer B would not be correct. Although biallelic CEBPA mutations are commonly identified in CEBPA-mutated AML, single mutations are not uncommon. Thus, although technically possible, answer C is not the best answer. The CEBPA protein exists as two primary isoforms, a full-length isoform (p42) and a shorter isoform (p30). Due to the fact that CEBPA has two translation initiation sites, the presence of a truncating N-terminal variant often results in a decrease of the p42 isoform and increase in the p30 isoform. This leads to an increased p30:p42 ratio which drives an immature cell state. Thus, D is the correct answer.

Correct answer:  B

Explanation of answer:  This is an abnormal signal pattern consisting of one intact (fused) signal, one 5’ (centromeric) signal, and one 3’ (telomeric) signal indicating a rearrangement of 22q12 (EWSR1) region; consistent with the diagnosis of Ewing’s sarcoma. PAX3::FOXO1 or PAX7::FOXO1 translocations are present in alveolar rhabdomyosarcoma. Spindle cell / sclerosing rhabdomyosarcoma may harbor MYOD1 mutations or VGLL2::NCOA2 rearrangements. Synovial sarcoma is characterized by a specific SS18::SSX fusion gene.

Correct answer: D

The clinical presentation suggests the causative gene is DICER1 which encodes a protein that facilitates microRNA production. microRNA is an important mechanism that regulates gene expression by silencing mRNA at post-transcription level.

Correct answer: B

Out of these options, for B-ALL t(12;21) is the only favorable prognosis. Hyperdiploid karyotype is also a favorable prognosis. 

Correct answer: A

Alterations commonly seen in myeloid malignancies include deletion 5q, 7q, monosomy 5, 7, trisomy 8, deletion 20q and deletion 17p/monosomy 17.

Correct answer: B

For a solid tumor, such as soft tissue tumor, the best tissue for cytogenetic testing by karyotype is the fresh tumor tissue. The FFPE is fixed and therefore cannot be cultured. The frozen will most likely not grow as the cells are dormant/dead. The blood will not have tumor cells that can be cultured.

Correct answer: B

This patient has both heterozygous and homozygous deletion of 13q14. This is a common finding in CLL. Patients with a 13q deletion as the sole abnormality detected by FISH generally have the longest survival time. Prognosis for patients with a homozygous 13q deletion is not significantly different than for a heterozygous 13q deletion (PMID: 22139735). Some newer data suggests that larger deletions may have less favorable outcomes (PMID: 34522485).

Correct answer: D

The inv(3)(q21q26) is often associated with a fusion between RPN1 and MECOM (MDS1 AND EVI1 COMPLEX LOCUS). It has been described in AML and MDS. Monosomy 7 is a common secondary abnormality. It is associated with a negative impact on prognosis.

Correct Answer: C

In general, "critical records" for cytogenetic testing are kept for 20 years. However, there is variability depending on the technology utilized and reason for referral.

Current guidelines specify the following retention times:

• Processed patient specimens and/or cell pellets – 2 weeks after report has been signed
• Stained slides (e.g., G-banding) – 3 years
• Neoplastic FISH Images – 10 years
• Images (chromosome analysis/non-neoplastic FISH) – 20 years
• Array – recommended that primary data be stored for at least 2 years and the analysis file + final clinical report be kept for “as long as possible”

(Shao, et al., 2021)

Correct answer: A
 

CHIP is associated with aging in hematopoietic stem and progenitor cells and the most commonly variants have been seen in DNMT3A, TET2, ASXL1, JAK2 and TP53. TP53 is one of the most commonly tested gene in hereditary cancer panel, therefore, skewed allele frequency in TP53 may indicate an event of CHIP, which needs to be differentiated from Li-Fraumeni syndrome. PMID: 31827082