Chromosomal Translocations Research Articles

From cytogenetics to cytogenomics: a new era in the diagnosis of chromosomal abnormalities in domestic animals.

Identification of chromosomal abnormalities is an important issue in animal breeding and veterinary medicine. Routine cytogenetic diagnosis of domestic animals began in the 1960s with the aim of identifying carriers of centric fusion between chromosome 1 and 29 in cattle. In the 1970s, chromosome banding techniques were introduced, and in the 1980s, the first cytogenomic techniques, based on the development of locus- and chromosome-specific probes, were used. Since the beginning of the twenty-first century, molecular techniques (such as polymorphism of microsatellite markers, droplet digital PCR, SNP microarrays, and whole genome sequencing) have begun to be widely used in animal breeding. This review is focused on the cytogenomic diagnosis of chromosome abnormalities in cattle, horses, pigs, dogs, and cats. We show that these approaches are very useful in large-population screening studies of the prevalence of aneuploidies (mainly of sex chromosomes) and structural rearrangements (centric fusions and reciprocal translocations).

Maternally Derived Complex Small Supernumerary Marker Chromosome 22 Associated with Cat-Eye Syndrome Like Features

Cat-eye syndrome (CES) is a rare genetic disease first reported in 1965. The estimated prevalence of CES is 1:50,000 to 1:150,000, and it is typically associated with an inverted duplicated small supernumerary marker chromosome (sSMC) derived from chromosome 22. The specific chromosomal band involved in CES causing partial tetrasomy is 22q11.21, where chromosomal rearrangements occur due to the presence of low-copy repeats (LCR22). The phenotype of CES is extremely diverse, ranging from normal to multiple abnormalities including intellectual disabilities and dysmorphic features. To our knowledge, over 340 patients with CES have been reported to date. This study reports a patient displaying a duplication of chromosome 22pter-22q12 involving band 22q11.21 where the CES critical region is located, and 18pter to 18p11. The propositus is a three-year-old girl, born to an unrelated and healthy couple. She was referred for facial dysmorphism and psychomotor delay. Banding cytogenetic analysis revealed an sSMC resulting from abnormal 3:1 segregation of the maternal balanced translocation t(18;22). Furthermore, the origin of the sSMC was confirmed by fluorescence in situ hybridization technique. The current study emphasized the importance of molecular cytogenetic techniques such as FISH in apprehending chromosomal abnormality. In addition, it shows that partial trisomy 22q11.2 to 22q12 may lead to CES-like symptoms.

Monogenic Diseases and IVF: Their Challenge in Emerging Technology

Objectives: Spontaneous abortions are often associated with chromosomal abnormalities, mitochondrial diseases, anatomical disorders, or infections and require investigation. In vitro fertilization (IVF) is known as an effective method for parents with chromosomal abnormalities to have children, but it should be evaluated in every case. Theoretical Framework: Congenital myopathies are a group of clinically, genetically, and histopathologically heterogeneous conditions characterized by pathological structural changes in muscle fibers. These diseases are monogenic and can sometimes occur even in IVF pregnancies. Method: A 3-month-old male infant was weak and unable to hold his head up. The baby, the first surviving child from the family's 7th pregnancy. Chromosomal analysis was performed on the mother and father. A balanced translocation t(5;9) was detected in the father. In the seventh pregnancy, IVF and all prenatal genetic screenings were performed. The baby was born on time and via cesarean section. Whole exome sequencing (WES) performed on the patient identified a pathogenic variant in the TMP3 gene. The patient's clinical presentation was consistent with congenital myopathy 4B(CMYP4B). Results and Discussion: It may not always be possible to identify monogenic diseases. In such cases, IVF pregnancies will also carry risks. Research Implications: Chromosomal abnormalities, mitochondrial diseases, and anatomical disorders sometimes occur even in IVF pregnancies. In such cases, IVF pregnancies will also carry risks. Originality/Value: Even if IVF pregnancies are considered thoroughly planned, they carry risks despite the current and developing treatment we have. More detailed information, including healthcare professionals, may be needed on this subject.

A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition.

Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the four haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploid U. brizantha and the other 18 from either U. ruziziensis or diploid U. decumbens. We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.

Balanced Translocation t(3;12) Disrupting HMGA2 and NAALADL2 Genes in Twins With Silver-Russell Syndrome and Intellectual Disability.

Silver-Russell Syndrome (SRS) is a genetic disorder characterized by intrauterine and postnatal growth restriction. Most cases are caused by an imprinting error either with hypomethylation of the Imprinted Control Region 1 at 11p15.5, or maternal uniparental disomy of chromosome 7. Approximately 40% of the cases have unknown etiology, thus distinct mechanisms have been described in association with the syndrome. Here, we present a case of monozygotic twin sisters with a clinical diagnosis of SRS, mild intellectual disability and epilepsy who carry a balanced translocation between chromosomes 3 and 12 that interrupts the NAALADL2 and HMGA2 genes, respectively. Disruption of HMGA2, a gene previously described as causative of SRS, confirms the initial diagnosis. NAALADL2 gene has been recently proposed as a candidate for intellectual disability and could partially contribute to our patient's phenotype.

Zebrafish modeling of atypical PML-RARA isoform from acute promyelocytic leukemia patient and its implications for clinical treatment.

Acute promyelocytic leukemia (APL) is driven by the specific fusion gene PML-RARA produced by chromosomal translocation. Three classic isoforms, L, V, and S, are found in more than 95% of APL patients. However, atypical PML-RARA isoforms are usually associated with uncertain disease progression and treatment prognosis. Recently, we found a novel PML-RARA isoform (named PA) in a patient with atypical clinical characteristics of APL. In order to provide valuable insights for clinical treatment, we constructed the novel PML-RARA isoform zebrafish model for all-trans retinoic acid (ATRA) treatment experiments and comparison with classical isoforms. We found that the effect of PA PML-RARA on the expression of neutrophil-related genes was comparable with classical isoforms and ATRA treatment worked successfully in the zebrafish model. Sequence and structure analysis of the PA protein confirmed its similarity to classical isoforms and the fusion site of PA PML-RARA did not affect the ATRA binding site. As expected, the patient achieved complete remission within two months of treatment with ATRA in combination with arsenic trioxide (ATO) and had a favorable prognosis during the three-year follow-up. Our study highlights the accuracy and efficacy of the PML-RARA zebrafish model in combination with protein structure prediction in support of clinical treatment strategies.

Identification of a cryptic unbalanced translocation Der(22)t(12;22)(q24.33;q13.33) in a large Chinese family with Phelan-McDermid syndrome by nanopore sequencing

To explore the genetic cause of a four-generation severe intellectual disability in a Chinese family using nanopore sequencing and to provide genetic counseling and reproductive guidance for family members. Multiple genetic analyses of the proband and family members were performed, including chromosome karyotype analysis, whole exome sequencing, nanopore sequencing, PCR amplification, and Sanger sequencing. The results of G-binding karyotyping, CGG repeats for FMR1, GGC repeats for NOTCH2NCL, and trio-whole-exome sequencing were negative for the proband and his parents. Nanopore sequencing showed that the proband carried 12q24.33 microduplication (3.26 Mb) and 22q13.33 microdeletion (1.5 Mb). According to the guidelines of the American Society for Medical Genetics and Genomics (ACMG), the 22q13.33 microdeletion was classified as pathogenic, whereas the 12q24.33 microduplication was classified as a variant of uncertain significance (VUS). The precise karyotype and location of chromosomal breakpoints in the patient and family members were determined through PCR. According to the results of Sanger sequencing, a cryptic balanced translocation was detected in the proband’s father. Additionally, informative SNPs were identified near the breakpoints for preimplantation genetic testing for structure rearrangement (PGT-SR) treatment by nanopore sequencing. We identified a cryptic unbalanced translocation in a large Chinese family with Phelan-McDermid syndrome (22q13.33 deletion syndrome) by nanopore sequencing. Nanopore sequencing can be a powerful tool for the genetic diagnosis of unexplained intellectual disability and the detection of precise breakpoints of chromosomal rearrangement in PGT-SR treatment.

Some Tumours Can Drive You Nuts: An Enigmatic Case of Metastatic Lymph Node

Introduction: NUT carcinoma (NC) is a rare aggressive undifferentiated malignant neoplasm. It can arise from midline and non-midline structures with no predilection for age and gender. NC is due to NUT gene rearrangement (Chromosomal translocation). The diagnosis is established by NUTM1 protein expression by IHC / FISH / NGS RNA sequencing Given the rarity and novelty, herein we discuss our case of NC. Aim: To establish a diagnosis of NUT carcinoma and its diagnostic challenges. Clinical History: A 23-year-old young male presented with complaints of right neck swelling. Results: Histopathology revealed a poorly differentiated malignant neoplasm. Immunohistochemistry showed diffuse positivity for NUTM1 protein, hence was reported as NUT carcinoma. Conclusion: It is an aggressive malignant neoplasm with a dismal prognosis. An integrated approach by clinicians, radiologists and pathologists is required for accurate diagnosis and timely management.

Reciprocal translocation experiments reveal gut microbiome plasticity and host specificity in a Qinghai-Xizang Plateau lizard.

Animal adaptation to environmental challenges is a complex process involving intricate interactions between the host genotype and gut microbiome composition. The gut microbiome, highly responsive to external environmental factors, plays a crucial role in host adaptability and may facilitate local adaptation within species. Concurrently, the genetic background of host populations influences gut microbiome composition, highlighting the bidirectional relationship between host and microbiome. Despite this, our understanding of gut microbiome plasticity and its role in host adaptability remains limited, particularly in reptiles. To clarify this issue, we conducted a reciprocal translocation experiment with gravid females of the Qinghai toad-headed lizards ( Phrynocephalus vlangalii) between high-altitude (2 600 m a.s.l.) and superhigh-altitude (3 600 m a.s.l.) environments on Dangjin Mountain of the Qinghai-Xizang Plateau, China. One year later, we assessed the phenotypes and gut microbiomes of their offspring. Results revealed significant plasticity in gut microbiome diversity and structure in response to contrasting elevations. High-altitude conditions increased diversity, and maternal effects appeared to enable high-altitude lizards to maintain elevated diversity when exposed to superhigh-altitude environments. Additionally, superhigh-altitude lizards displayed distinct gut microbiome structures with notable host specificity, potentially linked to their lower growth rates. Overall, these findings underscore the importance of the gut microbiome in facilitating reptilian adaptation to rapid environmental changes across altitudinal gradients. Furthermore, this study provides critical insights into microbial mechanisms underpinning local adaptation and adaptative plasticity, offering a foundation for future research on host-microbiome interactions in evolutionary and ecological contexts.

A multivalent engagement of ENL with MOZ.

The epigenetic cofactor ENL (eleven-nineteen-leukemia) and the acetyltransferase MOZ (monocytic leukemia zinc finger) have vital roles in transcriptional regulation and are implicated in aggressive forms of leukemia. Here, we describe the mechanistic basis for the intertwined association of ENL and MOZ. Genomic analysis shows that ENL and MOZ co-occupy active promoters and that MOZ recruits ENL to its gene targets. Structural studies reveal a multivalent assembly of ENL at the intrinsically disordered region (IDR) of MOZ. While the extraterminal (ET) domain of ENL recognizes the canonical ET-binding motif in IDR, the YEATS domains of ENL and homologous AF9 bind to a set of acetylation sites in the MOZ IDR that are generated by the acetyltransferase CBP (CREB-binding protein). Our findings suggest a multifaceted acetylation-dependent and independent coupling of ENL, MOZ and CBP/p300, which may contribute to leukemogenic activities of the ENL-MOZ assembly and chromosomal translocations of ENL, MOZ and CBP/p300.

Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes.

A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially in the sex chromosome chain. Therefore, the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex. Here, we present a new long reads-based chromosome-level short-beaked echidna (Tachyglossus aculeatus) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between 1 Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes. The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.

Loss of SMAD1 in acute myeloid leukemia with KMT2A::AFF1 and KMT2A::MLLT3 fusion genes.

KMT2A-rearrangements define a subclass of acute leukemias characterized by a distinct gene expression signature linked to the dysfunctional oncogenic fusion proteins arising from various chromosomal translocations involving the KMT2A (also known as MLL1) gene. Research on the disease pathomechanism in KMT2A-rearranged acute leukemias has mainly focused on the upregulation of the stemness-related genes of the HOX-family and their co-factor MEIS1. Here we report the KMT2A::AFF1 and KMT2A::MLLT3 fusion gene-dependent downregulation of SMAD1, a TGF-β signaling axis transcription factor. SMAD1 expression is lost in the majority of AML patient samples and cell lines containing the two fusion genes KMT2A::AFF1 and KMT2A::MLLT3 compared to non-rearranged controls. Loss of SMAD1 expression is inducible by introducing the respective two KMT2A fusion genes into hematopoietic stem and progenitor cells. The loss of SMAD1 correlated with a markedly reduced amount of H3K4me3 levels at the SMAD1 promoter in tested cells with KMT2A::AFF1 and KMT2A::MLLT3. The expression of SMAD1 in cells with KMT2A::AFF1 fusion genes impacted the growth of cells in vitro and influenced engraftment of the KMT2A::AFF1 cell line MV4-11 in vivo. In MV4-11 cells SMAD1 expression caused a downregulation of HOXA9 and MEIS1, which was reinforced by TGF-β stimulation. Moreover, in MV4-11 cells SMAD1 presence sensitized cells for TGF-β mediated G1-arrest. Overall, our data contributes to the understanding of the role of TGF-β signaling in acute myeloid leukemia with KMT2A::AFF1 by showing that SMAD1 loss can influence the growth dynamics and contribute to the pathogenic expression of disease driving factors.

Influence of the Sex of Translocation Carrier on Clinical Outcomes of Couples Undergoing Preimplantation Genetic Testing.

This study investigated the impact of the carrier on transferable blastocyst rate and live birth outcomes in couples with structural chromosomal abnormalities. Couples were grouped into reciprocal translocation, Robertsonian translocation, or inversions groups, and clinical data were retrospectively analyzed. Preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) was conducted, and pregnancy outcomes were compared. Embryo euploidy rates between male and female carriers differed nonsignificantly in the reciprocal translocation and inversion groups but significantly among the three groups. In the Robertsonian translocation group, male carriers had a higher embryo euploidy rate than that of female carriers. Sperm density of male carriers with reciprocal and Robertsonian translocation was significantly lower than that of the female carrier in the same group, whereas the difference was non-significant in the inversion group. The clinical outcomes of embryo transfer post-PGT were similar regardless of the sex of carriers with structural chromosomal abnormalities. Female carriers with Robertsonian translocations displayed a higher risk of producing embryos with chromosomal abnormalities than male carriers. Pregnancy, live birth, and cumulative live birth rates following a PGT-SR cycle were similar, irrespective of chromosomal structural rearrangement type, and carrier sex. Our findings offer valuable information for genetic counseling.

Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae.

Chromosomal rearrangements (CRs) often cause phenotypic variations. Although several major rearrangements have been identified in Triticeae, a comprehensive study of the order, timing, and breakpoints of CRs has not been conducted. Here, we reconstruct high-quality ancestral genomes for the most recent common ancestor (MRCA) of the Triticeae, and the MRCA of the wheat lineage (Triticum and Aegilops). The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060, respectively, which were arranged in their ancestral order. By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes, we revisit the rye chromosome structural evolution and propose alternative evolutionary routes. The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu are found to have occurred independently and are unlikely the result of chromosomal introgression following distant hybridization. We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event. Lastly, we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution, representing potential CR hotspots. This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.

Reproductive Risk Estimation Calculator for Balanced Translocation Carriers: An Improved Web-based Resource for Medical Genetics Professionals.

Balanced translocation carriers experience elevated reproductive risks, including pregnancy loss and children with anomalies due to generating chromosomally unbalanced gametes. While understanding the likelihood of producing unbalanced conceptuses is critical for individuals to make reproductive decisions, risk estimates are difficult to obtain as most balanced translocations are unique. To improve reproductive risk estimates, Drs. Trunca and Mendell created models based on a logistic regression analysis of a dataset of over 6000 individuals from over 1000 translocation families. While risk assessments using these models have been offered as a free service for years, this protocol aims to create a sustainable model for genetics professionals to obtain risk estimates for their patients directly. This protocol guides the user through collecting clinical information, using a risk-generating calculator based on the models, and interpreting the calculator outputs. This version of the protocol has been updated from the initial publication to introduce an additional resource to the community that is intended to improve accessibility and reduce error in calculating risks. In addition to the previously offered custom Java program, a web-based calculator that calculates age-adjusted miscarriage risks is now available. A practice tutorial is provided for both versions of the calculator to ensure competency in interpretation prior to use. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Estimation of reproductive risks for balanced translocation carriers Basic Protocol 2: Practical examples of typical patient encounters with instructive interpretations.

A variant W chromosome in Centromochlus heckelii (Siluriformes, Auchenipteridae) and the role of repeated DNA in its heteromorphism.

Centromochlus heckelii has the lowest diploid chromosome number (2n = 46) and the only described heteromorphic sex chromosome system in Auchenipteridae. This study presents a population of C. heckelii from the Central Amazon basin with subtle variations in the karyotype composition and a variant W chromosome with distinct morphology and increased C-positive heterochromatin content. In this population, the W chromosome is subtelocentric, whereas the only previous study on C. heckelii reported a metacentric W chromosome. Constitutive heterochromatin (CH) and accumulation of microsatellite motifs have significantly contributed to this W chromosome enlargement. Notably, this population exhibits numerous interstitial telomeric sites (ITSs). Some of these ITSs might represent genuine chromosomal fusion points due to the reduced 2n; however, additional mechanisms, such as chromosomal inversions, translocations, transpositions, or association with satellite DNA, are likely responsible for this unusual pattern. The 18S rDNA sites were found in both the Z and W chromosomes of all individuals. However, two individuals exhibited an additional 18S rDNA site in a single homologous of the chromosome pair 20, characterizing an intrapopulation polymorphism. The 5S rDNA sites were found in two chromosome pairs, distinguishing this population from other Centromochlinae species and further supporting it as one of the most efficient cytotaxonomic markers within the subfamily.

Functional Traits and Species Identity Drive Decomposition Along a Successional Gradient in Upper Andean Tropical Forests

ABSTRACTLeaf litter decomposition constitutes one of the most vital processes for maintaining productivity and carbon release in ecosystems. However, this remains one of the least understood processes in upper Andean tropical forests (UATF), a highly diverse ecoregion that has undergone extensive transformation over the centuries. In this study, we aimed to determine the relationships between decomposition rates of leaf litter, leaf functional traits, and microclimatic conditions along a successional gradient of UATF. We also tested the “after‐life effect” by analyzing changes between green and senescent leaves. We performed a fully reciprocal translocation experiment with 15 representative species of UATF in a set of 14 permanent plots by using 2520 litterbags distributed across 42 experimental units (three litterbeds per plot), over 1.5 years, with four harvesting times (3, 6, 12, and 18 months). Chemical and physical traits were measured in green and senescent leaves to identify the best predictors of decomposition and to analyze the “after‐life effect.” We found that functional traits and species identity drive litter decomposition in UATF, rather than succession and microclimatic conditions of soil moisture and temperature. The relative importance of traits was prevalent in all stages of decay, despite being stronger in the early phases. Although we found an “after‐life effect” of green leaves in decomposition, changes in chemical composition from green to senescent leaves indicated substantial nitrogen resorption, which is a limiting resource in tropical montane forests. With the increasing landscape transformation in UATF, changes in plant species composition could have profound impacts by altering decomposition rates, nutrient cycling, and global carbon storage.

Pollination ecotypes and the origin of plant species.

Ecological niche shifts are a key driver of phenotypic divergence and contribute to isolating barriers among lineages. For many groups of organisms, the history of these shifts and associated trait-environment correlations are well-documented at the macroevolutionary level. However, the processes that generate these patterns are initiated below the species level, often by the formation of ecotypes in contrasting environments. Here, I review the evidence in plants for 'pollination ecotypes' as microevolutionary responses to environmental gradients in pollinator availability. Pollinators are critical for population establishment and persistence in most species, thereby forming part of their fundamental niche. Novel floral trait combinations allow species to exploit particular pollination opportunities in local habitats and evolve primarily through sexual selection due to their effects on mating success. I examine selected case studies on the evolution of pollination ecotypes, including self-pollinating forms, and use these to illustrate challenging practical and conceptual issues. These issues include the paucity of reliable natural history data, the problem of implementing and interpreting reciprocal translocation experiments, and establishing criteria for when allopatric ecotypes should be considered species.

A comprehensive high-throughput screening approach for discovering inhibitors targeting the menin-MLL1 interaction.

The prognosis for mixed-lineage leukemia (MLL), particularly in young children, remains a significant health concern due to the limited therapeutic options available. MLL refers to KMT2A chromosomal translocations that produce MLL fusion proteins. The protein menin, which is essential for the malignant potential of these MLL fusion proteins, offers novel targets for acute leukemia treatment. This study reports the identification of potential new inhibitors of MLL-mediated leukemia targeting menin through the screening of two distinct drug libraries and existing inhibitors. The 3D structure of the protein was retrieved from the Protein Data Bank (ID: 8IG0). The drug libraries, sourced from public repositories such as the 'Epigenetic Drug Library' and 'The FDA-anticancer Drug Library,' yielded top candidates like Tozaseritib and Panobinostat, which exhibited the highest binding energy scores in the Glide virtual screening module. Additionally, 31 known menin-MLL1 inhibitors were identified through PDB screening and subsequently docked with the menin protein. The top three inhibitors (M-525, M-808, and MI-89) were selected for further analysis. Five menin-ligand complexes were validated using molecular dynamics analysis and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations to verify the stability and binding mechanisms.These findings provide insights into the molecular mechanisms of these drugs and lay the groundwork for future clinical development aimed at improving outcomes for acute myeloid leukemia (AML) patients.

TRACERx analysis identifies a role for FAT1 in regulating chromosomal instability and whole-genome doubling via Hippo signalling

Chromosomal instability (CIN) is common in solid tumours and fuels evolutionary adaptation and poor prognosis by increasing intratumour heterogeneity. Systematic characterization of driver events in the TRACERx non-small-cell lung cancer (NSCLC) cohort identified that genetic alterations in six genes, including FAT1, result in homologous recombination (HR) repair deficiencies and CIN. Using orthogonal genetic and experimental approaches, we demonstrate that FAT1 alterations are positively selected before genome doubling and associated with HR deficiency. FAT1 ablation causes persistent replication stress, an elevated mitotic failure rate, nuclear deformation and elevated structural CIN, including chromosome translocations and radial chromosomes. FAT1 loss contributes to whole-genome doubling (a form of numerical CIN) through the dysregulation of YAP1. Co-depletion of YAP1 partially rescues numerical CIN caused by FAT1 loss but does not relieve HR deficiencies, nor structural CIN. Importantly, overexpression of constitutively active YAP15SA is sufficient to induce numerical CIN. Taken together, we show that FAT1 loss in NSCLC attenuates HR and exacerbates CIN through two distinct downstream mechanisms, leading to increased tumour heterogeneity.