Advancing rare disease diagnosis and hereditary cancer research requires both cutting-edge technology and scientific collaboration. We’re pleased to highlight several recent publications from our customers, showcasing how comprehensive genomic analyses can uncover complex disease mechanisms that may be missed by conventional testing approaches. From identifying novel causes of childhood-onset neurodegeneration and hereditary haemorrhagic telangiectasia to expanding our understanding of constitutional MLH1 promoter methylation, these studies demonstrate the ongoing impact of innovative genetic research on patient care and diagnosis.
Title: Constitutional methylation of the MLH1 promoter: a case series including tumors not typically caused by Lynch Syndrome
Background:
Lynch syndrome (LS) is an inherited cancer predisposition syndrome, most commonly caused by pathogenic variants in the mismatch repair genes MLH1, MSH2, MSH6, or PMS2, and is associated with increased risks of colorectal and endometrial cancers. In 5–10% of LS-related cancers lacking detectable germline MMR-gene variants, constitutional MLH1 promoter methylation causes silencing of MLH1 and produces a clinical phenotype indistinguishable from that of germline MLH1 mutations.
Objective: This report describes the clinical features of four previously unpublished patients with primary constitutional MLH1 promoter methylation.
Subjects and Methods: Four unrelated patients with constitutional MLH1 promoter methylation were identified between 2010 and 2024 and underwent molecular characterization. DNA extracted from blood, normal tissue, and tumor tissue was analyzed using next-generation sequencing to screen MLH1 and other hereditary cancer genes, with variants interpreted according to established clinical guidelines and reference databases. MLH1 promoter methylation was assessed in bisulfite-treated DNA using droplet digital PCR, allowing quantification of methylation levels and confirmation of constitutional MLH1 methylation status.
Results: The four patients with constitutional MLH1 promoter methylation presented with a range of Lynch syndrome–associated cancers, including early-onset colorectal, endometrial, and multiple primary cancers, while one patient had isolated endometrial cancer. Notably, none of the families showed a strong history of Lynch syndrome–associated cancers, and testing of available relatives did not detect constitutional MLH1 methylation, suggesting these cases largely occurred in the absence of a clear familial pattern.
Conclusions: The authors observed considerable variation in methylation levels, including evidence of mosaicism in some patients, and found no underlying MLH1 promoter sequence variants, although rare familial transmission of primary constitutional MLH1 methylation has been reported. Because constitutional MLH1 methylation can be overlooked when MLH1 methylation is assumed to indicate a sporadic tumor, the study emphasizes the need for greater awareness and targeted testing, particularly in patients with MLH1-methylated colorectal or endometrial cancers diagnosed at a young age or in those with multiple tumors.
How VarSeq was used: Sequence alignment and variant calling for patients 1-3 were done using a GATK-pipeline and GRCh38; data were filtered to identify variants in the following genes (APC, AXIN2, BMPR1A, EPCAM, MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NTHL1, PMS2, POLD1, POLE, PTEN, RNF43, RPS20, SCG5, SMAD4, STK11, TP53) using VarSeq (Golden Helix). In patient 2 ATM, BARD1, BRCA1/2, BRIP1, CHEK2, PALB2, RAD51C/D were also analyzed.
Variants were interpreted using databases hosting frequencies (gnomAD), databases hosting known variants (InSiGHT, ClinVar, LOVD, HGMD) and gene specific guidelines developed by gene expert panels (ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 1.0.0) and ACMG guidelines [16]. MLH1 was screened in its entirety, including all exons, introns, and 5000 base pairs of the promoter region.
Citation: Graversen, L., Assenholt, J., Pedersen, I.S. et al. Constitutional methylation of the MLH1 promoter: a case series including tumors not typically caused by Lynch Syndrome. Eur J Hum Genet (2026). https://doi.org/10.1038/s41431-026-02149-z
Title: Recurrent t(9;12) translocation disrupting ACVRL1 intron 9 causes hereditary haemorrhagic telangiectasia missed by standard exome sequencing in four unrelated families
Background: Hereditary haemorrhagic telangiectasia (HHT) is an autosomal dominant vascular disorder most often caused by pathogenic variants in the ACVRL1 or ENG genes. While most causative variants are readily detected by standard next-generation sequencing, balanced structural rearrangements and deep intronic variants may be missed and could explain some genetically unresolved HHT cases.
Objective: This study investigated four unrelated families with clinical features of HHT in whom prior whole exome sequencing (WES) was inconclusive.
Subjects and Methods: This study focused on four unrelated families with clinically diagnosed HHT in whom prior whole-exome sequencing had not identified a causative variant. The presence of recurrent miscarriages and previously identified chromosomal abnormalities prompted a targeted reanalysis of genetic data, revealing potential disruption of HHT-associated genes.
Results: All four families carried the same apparently balanced translocation, t(9;12)(p21.2;q13.13), which disrupted a mutational hotspot within intron 9 of ACVRL1 and was identified as the likely cause of HHT. The translocation co-segregated with disease, was absent in unaffected relatives, and recurrent miscarriages served as an important clinical clue leading to cytogenetic testing and diagnosis.
Conclusions: A recurrent balanced translocation t(9;12)(p21.2;q13.13) disrupting intron 9 of ACVRL1 was identified as an undetectable-by-exome cause of HHT in previously unresolved cases, underscoring the need for broader genomic testing beyond standard exome sequencing.
How VarSeq was used: Sequencing reads were aligned to the human reference genome GRCh37/hg19. Bioinformatic analysis was performed using Data Genomics Software v1.20.0 (Health in Code, SL, Valencia, Spain). CNV analysis was conducted using VarSeq software (Golden Helix Inc., Bozeman, MT, USA). Variant filtering was restricted to a virtual panel of 10 HHT-associated genes: ACVRL1 (NM_000020.2), BMPR2 (NM_001204.6), ENG (NM_001114753.2), EPHB4 (NM_004444.4), GDF2 (NM_016204.3), PIK3CA (NM_006218.3), RASA1 (NM_002890.2), SMAD4 (NM_005359.5), SMAD6 (NM_005585.5) and TEK (NM_000459.4). A minimum coverage depth of >20x was achieved for 100% of the targeted exonic regions in BMPR2, PIK3CA, RASA1, SMAD4 and TEK. Coverage at >20x was >98% for GDF2, ENG and EPHB4 and >95% for SMAD6 and ACVRL1.
Citation: Esteve-Garcia, A., Madrigal, I., & Aguilera, C. (2026). Recurrent t(9;12) translocation disrupting ACVRL1 intron 9 causes hereditary haemorrhagic telangiectasia missed by standard exome sequencing in four unrelated families. European Journal of Internal Medicine, 106991. https://doi.org/10.1016/j.ejim.2026.106991
Title: Childhood-onset neurodegeneration with ataxia, tremor, optic atrophy, and cognitive decline (CONATOC): An integrated clinical series with genetic analysis
Background: Choline transporter CTL1 (encoded by SLC44A1) is essential for phospholipid synthesis and cellular membrane homeostasis, including in mitochondria and the central nervous system. Loss-of-function mutations in SLC44A1 cause a severe neurodegenerative disorder (CONATOC) due to impaired myelin formation and disrupted lipid metabolism, with animal studies further confirming CTL1’s critical role in oligodendrocyte function and CNS myelination.
Objective: This study integrates clinical, neuroimaging, functional, and genetic data from four patients to refine the phenotype and variant classification. It presents two newly identified cases and updated clinical and imaging data on two previously reported patients.
Subjects and Methods: Clinical and neuroimaging data were collected from four patients under ethical approval, and genomic analyses were performed using a combination of whole-exome sequencing, targeted gene panels, Sanger validation, and RNA sequencing to assess variants and transcript effects in SLC44A1. Functional consequences of identified variants were further evaluated in patient-derived fibroblasts by measuring choline and ethanolamine uptake using radiolabeled transport assays.
Results: This study shows that CONATOC is caused by SLC44A1 dysfunction leading to impaired choline and ethanolamine transport and a consistent pattern of white-matter disease with neurodegeneration. It highlights limited benefit from current supplementation and supports CTL1 as a key target for future diagnostic and therapeutic approaches.
Conclusions: This study highlights SLC44A1 as central to myelin biology and broadens the clinical spectrum of CONATOC. It supports a shared disease mechanism involving impaired choline transport and phospholipid metabolism and emphasizes the need for earlier diagnosis and development of targeted therapies.
How VarSeq was used: Patients B and C: As described previously [20], Patient C WES was performed on exome data obtained from Merck Research Labs, Boston. The sequence alignment was performed using GATK Best Practice pipeline v. 3.3–0 and variant/ annotation filtering were performed by VarSeq (Golden Helix). Variant significance was informed by PolyPhen-2, SIFT, and MutationTaster. Sanger sequencing of SLC44A1 exon 13 (RefSeq: NM_080546.4) was performed in the brother (Patient B) and parents.
Citation: Al Douri, S., Kibaek, M., & Gauquelin, L. (2026). Childhood-onset neurodegeneration with ataxia, tremor, optic atrophy, and cognitive decline (CONATOC): An integrated clinical series with genetic analysis. Brain Disorders, Volume 22, 100321. https://doi.org/10.1016/j.dscb.2026.100321
