Molecular Cytogenetic and Y Copy Number Analysis of a Reciprocal ECAY-ECA13 Translocation in a Stallion with Complete Meiotic Arrest

We present a detailed molecular cytogenetic analysis of a reciprocal translocation between horse (ECA) chromosomes Y and 13 in a Friesian stallion with complete meiotic arrest and azoospermia. We use dual-color fluorescence in situ hybridization with select ECAY and ECA13 markers and show that the translocation breakpoint in ECAY is in the multicopy region and in ECA13, at the centromere. One resulting derivative chromosome, Y;13p, comprises of ECAY heterochromatin (ETSTY7 array), a small single copy and partial Y multicopy region, and ECA13p. Another derivative chromosome 13q;Y comprises of ECA13q and most of the single copy ECAY, the pseudoautosomal region and a small part of the Y multicopy region. A copy number (CN) analysis of select ECAY multicopy genes shows that the Friesian stallion has significantly (p < 0.05) reduced CNs of TSPY, ETSTY1, and ETSTY5, suggesting that the translocation may not be completely balanced, and genetic material is lost. We discuss likely meiotic behavior of abnormal chromosomes and theorize about the possible effect of the aberration on Y regulation and the progression of meiosis. The study adds a unique case to equine clinical cytogenetics and contributes to understanding the role of the Y chromosome in male meiosis.

Characterization of a Rare Mosaic Unbalanced Translocation of t(3;12) in a Patient With Neurodevelopmental Disorders

Background Unbalanced translocations may be de novo or inherited from one parent carrying the balanced form and are usually present in all cells. Mosaic unbalanced translocations are extremely rare with a highly variable phenotype depending on the tissue distribution and level of mosaicism. Mosaicism for structural chromosomal abnormalities is clinically challenging for diagnosis and counseling due to the limitation of technical platforms and complex mechanisms, respectively. Here we report a case with a tremendously rare maternally-derived mosaic unbalanced translocation of t(3;12), and we illustrate the unreported complicated mechanism using single nucleotide polymorphism (SNP) array, fluorescence in situ hybridization (FISH), and chromosome analyses. Case Presentation: An 18-year-old female with a history of microcephaly, pervasive developmental disorder, intellectual disability, sensory integration disorder, gastroparesis, and hypotonia presented to our genetics clinic. She had negative karyotype by parental report but no other genetic testing performed previously. SNP microarray analysis revealed a complex genotype including 8.4 Mb terminal mosaic duplication on chromosome 3 (3p26.3->3p26.1) with the distal 5.7 Mb involving two parental haplotypes and the proximal 2.7 Mb involving three parental haplotypes, and a 6.1 Mb terminal mosaic deletion on chromosome 12 (12p13.33->12p13.31) with no evidence for a second haplotype. Adjacent to the mosaic deletion is an interstitial mosaic copy-neutral region of homozygosity (1.9 Mb, 12p13.31). The mother of this individual was confirmed by chromosome analysis and FISH that she carries a balanced translocation, t(3;12)(p26.1;p13.31). Conclusion Taken together, the proband, when at the stage of a zygote, likely carried the derivative chromosome 12 from this translocation, and a postzygotic mitotic recombination event occurred between the normal paternal chromosome 12 and maternal derivative chromosome 12 to “correct” the partial 3p trisomy and partial deletion of 12p. To the best of our knowledge, it is the first time that a mechanism utilizing a combined cytogenetic and cytogenomic approach, and we believe it expands our knowledge of mosaic structural chromosomal disorders and provides new insight into clinical management and genetic counseling.

A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular study

Background There are many reports on rearrangements occurring separately in the regions of chromosomes 9p and 15q affected in the case under study. 15q duplication syndrome is caused by the presence of at least one extra maternally derived copy of the Prader–Willi/Angelman critical region. Trisomy 9p is the fourth most frequent chromosome anomaly with a clinically recognizable syndrome often accompanied by intellectual disability. Here we report a new case of a patient with maternally derived unique complex sSMC resulting in partial trisomy of both chromosomes 9 and 15 associated with intellectual disability. Case presentation We characterise a supernumerary derivative chromosome 15: 47,XY,+der(15)t(9;15)(p21.2;q13.2), likely resulting from 3:1 malsegregation during maternal gametogenesis. Chromosomal analysis showed that a phenotypically normal mother is a carrier of balanced translocation t(9;15)(p21.1;q13.2). Her 7-year-old son showed signs of intellectual disability and a number of physical abnormalities including bilateral cryptorchidism and congenital megaureter. The child’s magnetic resonance imaging showed changes in brain volume and in structural and functional connectivity revealing phenotypic changes caused by the presence of the extra chromosome material, whereas the mother’s brain MRI was normal. Sequence analyses of the microdissected der(15) chromosome detected two breakpoint regions: HSA9:25,928,021-26,157,441 (9p21.2 band) and HSA15:30,552,104-30,765,905 (15q13.2 band). The breakpoint region on chromosome HSA9 is poor in genetic features with several areas of high homology with the breakpoint region on chromosome 15. The breakpoint region on HSA15 is located in the area of a large segmental duplication. Conclusions We discuss the case of these phenotypic and brain MRI features in light of reported signatures for 9p partial trisomy and 15 duplication syndromes and analyze how the genomic characteristics of the found breakpoint regions have contributed to the origin of the derivative chromosome. We recommend MRI for all patients with a developmental delay, especially in cases with identified rearrangements, to accumulate more information on brain phenotypes related to chromosomal syndromes.

A Unique Case of der(16)t(1;16) Identified in B-Lymphoblastic Leukemia

Introduction/Objective A derivative chromosome 16 is rare in hematologic malignancies. There are only two previously reported cases to date, both associated with acute myeloid leukemia (AML). In these cases, the t(1;16) presented as a der(16)t(1;16) resulting in trisomy 1q. This was the sole anomaly in each case. Cytogenetic abnormalities in B-ALL are common and important for understanding of the pathogenesis, classification and prognosis of the disease. Herein we describe a case of der(16)t(1;16)(q12;q24) identified for the first time in a patient with B-cell acute lymphoblastic leukemia (B-ALL), with correlation with morphologic and immunophenotypic findings. Methods/Case Report The patient is a 65 year-old male who initially presented with one week of fatigue. A complete blood count showed leukocytosis (white blood cell count of 24.6 x 103/uL), anemia (hemoglobin of 7.9 g/dL), marked thrombocytopenia (platelets of 5 x 103/uL). A differential showed 64% blasts and peripheral blood flow cytometry confirmed B-lymphoblastic differentiation, with two distinct immunophenotypic populations. The patient’s bone marrow biopsy was hypercellular (&gt;95% cellularity) with panhypoplasia and a marked increase in blasts (88% by aspirate manual differential). Cytogenetic analysis of the bone marrow also demonstrated the presence of two clonal cell lines. The first cell line was chromosomally normal, while the second had a t(9;22) translocation and a derived chromosomes 16 from a t(1;16). FISH analysis confirmed 59% of cells demonstrated a BCR/ABL1 fusion event. Results (if a Case Study enter NA) NA Conclusion The patient’s der(16)t(1;16)(q12;q24) represents a novel genetic abnormality that has not previously been reported in B-ALL. Although it has been described in other acute leukemias, little is known about this abnormality in B-ALL and its implications in pathogenesis and prognosis. Additional molecular testing, including chromosomal microarray analysis, mate-pair, or long-range DNA sequencing or RNA sequencing, could potentially identify the fusion partners and shed light on pathophysiological mechanisms implicated in the leukemic process.

Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin–Siris Syndrome

Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein, we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin–Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90-Mb pericentric and a 47-Mb paracentric inversion on a single chromosome. Subsequent analysis of short-read whole-genome sequencing data and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting ARID1B for which haploinsufficiency leads to the CSS1 disease trait (MIM:135900). The aggregate structural variant data show that the resolved, the resolved derivative chromosome architecture presents four de novo inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene ARID1B is shown to occur between the fourth and fifth exon of the canonical transcript with subsequent qPCR studies confirming a decrease in ARID1B expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient’s clinical phenotype or resolving unsolved Mendelian disease cases.

Complex approach to the study of the Derivative Chromosome 8

Введение. Дериватная хромосома (der) - структурно аномальная хромосома, формирование которой может происходить как в результате перестроек с участием двух и более негомологичных хромосом, так и вследствие аберраций внутри одной хромосомы. Дифференциальная диагностика дериватных хромосом очень важна для выяснения происхождения хромосомной аномалии и для определения тактики медико-генетического консультирования с целью оценки повторного риска рождения ребенка с хромосомным дисбалансом. В данной работе представлены семь случаев дериватной хромосомы 8, имеющих различное происхождение и механизмы формирования, а также протокол обследования пациентов с дериватной хромосомой 8 в кариотипе. Цель: изучить структуру и механизмы формирования дериватных хромосом 8. Методы: стандартное цитогенетическое исследование, M-FISH, MCB8, FISH с локус-специфичными субтеломерными ДНК-зондами, FISH с несерийными ДНК-зондами на район р23.1 хромосомы 8. Результаты. В результате проведенного стандартного цитогенетического исследования в кариотипе семи неродственных пробандов была обнаружена дериватная хромосома 8. При использовании цитогенетического и молекулярно-цитогенетического подходов было установлено, что у четырех пациентов дериватная хромосома 8 возникла в результате инвертированной дупликации/делеции 8р, а у трех - несбалансированной транслокации с участием хромосомы 8: der(8)t(8;17), der(8)t(8;12) и der(8)t(7;8). Во всех случаях был определен механизм формирования хромосомных перестроек. Дериватные хромосомы транслокационного происхождения в двух случаях были сформированы de novo, а в одном случае - как результат патологической мейотической сегрегации отцовской реципрокной транслокации. Все дериватные хромосомы с инвертированной дупликацией/делецией 8р были следствием эктопической рекомбинации. Заключение. Представленные результаты демонстрируют целесообразность комплексного лабораторного подхода в изучении структуры и происхождения дериватной хромосомы 8. Характеристика происхождения хромосомного дисбаланса является неотъемлемой частью обследования пациентов со структурно аномальной хромосомой 8 в кариотипе. Background. Derivative chromosome (der) is a structurally abnormal chromosome, the formation of which can occur as a result of rearrangements with the participation of two or more non-homologous chromosomes, or be the result of aberrations within one chromosome. Differential diagnosis of derivative chromosomes is very important for clarifying the origin of the chromosomal abnormality and for determining the tactics of medical genetic counseling in order to assess the repeated risk of chromosomal imbalance. This work presents seven cases of a derivative chromosome with different origins and mechanisms of formation, as well as a protocol for examining patients with derivative chromosome 8 in the karyotype. Aim: to study the structure and mechanisms of formation of the derivative chromosome 8. Methods. GTG-banded chromosomal analysis, M-FISH, MCB8, FISH with subtelomeric DNA probes, FISH with home-made DNA probes for 8p23.1. Results. As a result of a conventional cytogenetic study of seven unrelated probands a derivative chromosome 8 was found. In all cases, the mechanism of the formation of chromosomal rearrangements was determined. Derivative chromosomes of translocation origin were formed de novo in two cases- der(8)t(8;12) and der(8)t(7;8), and in one case -der(8)t(8;17) - as a result of malsegregation of the paternal reciprocal translocation. In the remaining four cases, the derivative chromosomes were identified as an inverted duplication/deletion 8p due to ectopic recombination. Conclusion. The presented results demonstrate the feasibility of an integrated laboratory approach in the diagnosis of derivative chromosome 8. Characterization of the origin of chromosomal imbalance is an integral part of the examination of patients with structurally abnormal chromosome 8 in the karyotype.

Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes

Derivative chromosome der(1;16), isochromosome 1q, and deleted 16q—producing arm-level 1q-gain and/or 16q-loss—are recurrent cytogenetic abnormalities in breast cancer, but their exact role in determining the malignant phenotype is still largely unknown. We exploited The Cancer Genome Atlas (TCGA) data to generate and analyze groups of breast invasive carcinomas, called 1,16-chromogroups, that are characterized by a pattern of arm-level somatic copy number aberrations congruent with known cytogenetic aberrations of chromosome 1 and 16. Substantial differences were found among 1,16-chromogroups in terms of other chromosomal aberrations, aneuploidy scores, transcriptomic data, single-point mutations, histotypes, and molecular subtypes. Breast cancers with a co-occurrence of 1q-gain and 16q-loss can be distinguished in a “low aneuploidy score” group, congruent to der(1;16), and a “high aneuploidy score” group, congruent to the co-occurrence of isochromosome 1q and deleted 16q. Another three groups are formed by cancers showing separately 1q-gain or 16q-loss or no aberrations of 1q and 16q. Transcriptome comparisons among the 1,16-chromogroups, integrated with functional pathway analysis, suggested the cooperation of overexpressed 1q genes and underexpressed 16q genes in the genesis of both ductal and lobular carcinomas, thus highlighting the putative role of genes encoding gamma-secretase subunits (APH1A, PSEN2, and NCSTN) and Wnt enhanceosome components (BCL9 and PYGO2) in 1q, and the glycoprotein E-cadherin (CDH1), the E3 ubiquitin-protein ligase WWP2, the deubiquitinating enzyme CYLD, and the transcription factor CBFB in 16q. The analysis of 1,16-chromogroups is a strategy with far-reaching implications for the selection of cancer cell models and novel experimental therapies.

A Case of Partial Trisomy of 10q and Partial Monosomy of 6p Resulting from Maternal t(6;10) (p23;q24)

Chromosomal analysis is practiced routinely since long time in congenital malformations to find out structural and or numerical chromosomal aberrations. Translocation is one of the structural chromosomal aberrations where exchange of genetic material between the chromosomes is seen because of two breakpoints. On the basis of involvement of type of chromosome, two different types of translocation are defined. A case of two-year-old girl child with the history of developmental delay, generalised hypotonia and recurrent infections was reported whose cytogenetic analysis showed additional genetic material on ‘p’ arm of one chromosome 6. To find out the additional genetic material, parental chromosomal study was done which revealed balanced translocation between ‘q’ arm of chromosome 10 and ‘p’ arm of chromosome 6 and normal chromosomal pattern in father. Balanced translocation in mother gave rise to formation of derivative chromosome 6 which was transmitted to daughter causing partial trisomy of 10q and partial monosomy of 6p. This gain and loss of genetic material could be the cause of phenotypic features. In the current case, karyotyping was an investigation of choice and offering genetic counselling regarding prenatal diagnosis in future pregnancy was a thoughtful step.

Unscrambling cancer genomes via integrated analysis of structural variation and copy number

Complex somatic genomic rearrangement and copy number alterations (CNA) are hallmarks of nearly all cancers. Whilst whole genome sequencing (WGS) in principle allows comprehensive profiling of these events, biological and clinical interpretation remains challenging. We have developed LINX, a novel algorithm which allows interpretation of short-read paired-end WGS derived structural variant and CNA data by clustering raw structural variant calls into distinct events, predicting their impact on the local structure of the derivative chromosome, and annotating their functional impact on affected genes. Novel visualisations facilitate further investigation of complex genomic rearrangements. We show that LINX provides insights into a diverse range of structural variation events including single and double break-junction events, mobile element insertions, complex shattering and high amplification events. We demonstrate that LINX can reliably detect a wide range of pathogenic rearrangements including gene fusions, immunoglobulin enhancer rearrangements, intragenic deletions and duplications. Uniquely, LINX also predicts chained fusions which we demonstrate account for 13% of clinically relevant oncogenic fusions. LINX also reports a class of inactivation events we term homozygous disruptions which may be a driver mutation in up to 8.8% of tumors including frequently affecting PTEN, TP53 and RB1, and are likely missed by many standard WGS analysis pipelines.