Instituto de Medicina Genómica

The combination of hearing loss and visual impairment in a single patient strongly suggests a genetic aetiology. However, after conventional testing, a considerable proportion of deafblindness cases remain without a genetic diagnosis. The aim of this study was to address this diagnostic gap. We developed an enhanced exome strategy that uses a whole-exome backbone complemented by spike-in capture probes for (i) low-coverage coding segments and clinically validated, non-coding regions (including deep intronic splice-altering sites and untranslated exonic sequences) across 659 genes associated with hearing loss and/or visual impairment, and (ii) mitochondrial DNA. With 66.6 million paired-end reads per sample, this methodology achieved coverage of at least 20 reads per base at 99.3% of target coding and non-coding positions of genes associated with deafness and/or blindness, as well as 98.8% of the whole exome. The enhanced exome approach correctly identified the genetic variants causative of deafness and/or blindness in 10 out of 10 cases with a previously known genetic cause, in 3 out of 10 additional cases that remained undiagnosed after extensive panel sequencing, and in 4 out of 4 cases that had not been genetically studied before. Comparison of the performance of two commercial bioinformatics platforms for enhanced exome interpretation revealed that eVAI consistently prioritised causative variants higher than, or as high as, VarSome Clinical, resulting in a tendency toward shorter interpretation times using the former. Both platforms offered the same diagnostic yield and both failed to correctly call one of the causative variants. In an era where many centres operate exome analysis through virtual panels, enhanced exome sequencing leverages the advantages of whole-exome and custom panel sequencing: it provides panel-like sensitivity for clinically actionable loci, while offering the flexibility to periodically reanalyse data and discover candidate genes.

Primary Sjögren's syndrome (pSS) is an autoimmune disease characterized by inflammation and damage to salivary and lacrimal glands. Its etiology involves both genetic and environmental factors. Among susceptibility genes, IRF5 has been highlighted in European populations, but evidence in non-European groups remains limited. This study evaluated whether IRF5 variants rs2004640G/T, rs2070197T/C, rs10954213G/A, and rs59110799G/T are associated with pSS susceptibility, clinical manifestations, or the presence of autoantibodies in a Mexican population. The diagnosis was confirmed by rheumatologists using the 2016 ACR-EULAR classification criteria for pSS. Genotyping was performed using TaqMan probes in 231 controls and 132 pSS patients from central Mexico. Associations were analyzed through binary logistic regression under different genetic models, adjusting for age and geographic origin. Clinical correlations were examined with SNPStats, and haplotypes were constructed using Haploview. Results showed that all four IRF5 variants were significantly associated with pSS susceptibility. Moreover, rs2004640, rs2070197, and rs10954213 variants were associated with arthritis, a frequent clinical manifestation in pSS patients. This represents the first evidence in a Latin American population demonstrating that IRF5 variants contribute to increased risk of developing pSS. These findings suggest ethnicity-specific genetic influences and highlight the importance of expanding research beyond European cohorts. Replication in larger samples and functional analyses are needed to confirm these associations and clarify their biological relevance.

Nuestro sistema inmune puede reconocer y destruir células tumorales; sin embargo, los tumores han desarrollado estrategias altamente sofisticadas para esquivar este ataque. Por ejemplo, las células tumorales pueden camuflarse volviéndose invisibles al patrullaje inmunitario y, en caso de ser detectadas, pueden manipular a las células inmunes para que dejen de funcionar o incluso provocar que se destruyan. Además, los tumores también pueden modificarse a sí mismos y volverse más resistentes sobreviviendo al ataque inmunitario. Comprender estos mecanismos de evasión es clave para el desarrollo de terapias innovadoras en oncología.

The whole genome amplification (WGA) allows new clinical applications with minimal genetic material, such as in the genetic diagnosis of Mendelian diseases in embryos before implantation (Preimplantation Genetic Test for Mendelian Abnormalities, PGT-M). This approach allows couples to avoid the transmission of Mendelian disease by undergoing assisted reproduction treatment through in vitro fertilization (IVF). First, Preimplantation Genetic Testing for Aneuploidy (PGT-A) is used to identify chromosomal aneuploidies in IVF-generated embryos. Then, or in parallel, euploid embryos can be screened for specific diseases caused by variants in a single gene to achieve the conception of offspring free of a specific monogenic disease.Here, we detail the WGA preparation and two downstream usages: (1) preparation of PCR fragments for Sanger sequencing, exemplifying the diseases we detected for healthy embryo selection and transfer in IVF, and (2) detection of chromosome Y for embryo sex diagnosis.

Inborn errors of immunity (IEIs) are a heterogeneous group of disorders, genetically diverse but phenotypically overlapping. Over 500 IEI-related genes have been identified. Next generation sequencing (NGS) enables the simultaneous evaluation of a large number of genes in multiple patients in parallel. Since 2017, in our setting, custom IEI panels have been useful mainly for patients displaying clinical phenotypes of immune dysregulation and autoinflammatory disorders. Our aim is to evaluate the performance of targeted NGS panels based on International Union of Immunological Societies (IUIS) gene categories by examining how many patients achieved a conclusive diagnosis. A retrospective analysis was performed on 361 index cases submitted to four chronologically successive targeted NGS custom panels. The first panel included 124 IUIS genes, most of them related to autoimmune and immune dysregulation disease categories. The second panel contained 143 IUIS genes, including defects of innate immunity. The third and fourth, large panels covering 314 and 325 IUIS genes, respectively, included/comprised the majority of IUIS disease categories, with focus on autoinflammatory, immune dysregulation, and intrinsic immunity disease categories. From a total of 361 samples studied, 264 were referred due to clinical suspicion of immune dysregulation, autoinflammatory disease, or defects in innate immunity. Twenty-three percent of them (61/264) achieved a confirmed or highly probable genetic etiology. According to the main IEI IUIS disease categories included in targeted panels, immune dysregulation represented 26% (32/123) of these diagnoses, autoinflammatory disorders 21% (18/85), and defects in innate immunity 19% (11/56). In the remaining patients studied, 42% (41/97) of them achieved a conclusive diagnosis in others IEI IUIS disease categories. The NGS approach demonstrated the expected IEI diagnostic rate. The strategy of designing panels oriented toward IEI disease categories that present the greatest variability in clinical presentations with overlapping phenotypes proved to be effective regarding achievement of conclusive diagnoses in our cohort.

BackgroundThree-dimensional (3D) culture captures key features of tumor architecture and microenvironmental signaling. Because microRNAs (miRNAs) are central post-transcriptional regulators, we asked whether 3D growth would reveal disease-relevant lncRNA-miRNA-mRNA programs in BT-474 luminal breast cancer cells.MethodsBT-474 cells were profiled with GeneChip miRNA 4.0 microarrays to compare 3D versus 2D conditions. We then performed an integrative analysis consisting of: (i) extracting miRNA–mRNA interactions from miRNet and ENCORI (predicted and curated) for the differentially expressed miRNAs; (ii) identifying inverse miRNA–mRNA pairs (miRNA downregulated with target mRNA upregulated, or the reverse) using public mRNA data from BT-474 3D versus 2D cultures so that pairs were consistent with regulatory repression; and (iii) retaining only those miRNA–mRNA pairs that also appeared in miRNet/ENCORI. In a separate step, we examined public luminal breast tumor datasets versus BT-474 2D cultures to determine which 3D-identified miRNAs showed a similar direction of expression change in luminal tumors, thereby prioritizing signals with putative in vivo relevance. Finally, to enhance biological plausibility, we incorporated an lncRNA layer by leveraging their miRNA “sponge” (ceRNA) activity, and we assembled an integrated miRNA–mRNA–lncRNA network. Key miRNAs from this network were then evaluated for expression in external TCGA cohorts and for diagnostic potential using area-under-the-curve (AUC) analysis.ResultsOur data reveal a reprogramming of miRNA expression between 3D and 2D cultures. Using a threshold of FC > 1.5 and p < 0.05, we found 75 miRNAs upregulated and 82 downregulated in 3D relative to 2D. To strengthen biological interpretation, we integrated our miRNA expression data with public mRNA profiles from BT-474 cells cultured in 3D versus 2D. We then cross-referenced interactions reported in miRNet and ENCORI, retaining only miRNA–mRNA pairs showing inverse regulation. This integrative layer yielded a pathway-level view in which 3D-modulated miRNAs collectively favored proliferative programs, ESR1/estrogen signaling, MAPK/JNK activity, cell-cycle control, and extracellular-matrix remodeling, with relative attenuation of EGFR/TGF-β signaling. Together, the inferred miRNA–mRNA network supports a shift toward a more tumor-like, transcriptionally active state in 3D. To reinforce translational relevance, we cross-referenced public luminal breast tumor datasets with BT-474 2D cultures and identified 14 miRNAs in common, with the same direction of change as observed in 3D cultures. From these, we assembled co-regulatory networks linking miRNAs to their mRNA targets and to lncRNAs. This analysis highlighted four key miRNA nodes: miR-92a-3p, miR-539-5p, miR-18a-5p, and miR-130a-3p, which are connected to 58 mRNAs and modulated by 12 lncRNAs. The hubs converge on pathways for growth and survival via the RTK–MAPK axis, estrogen signaling, and fibronectin/adhesion–mechanotransduction processes, depicting a proliferative, mechano-responsive phenotype. Additionally, these miRNAs emerged as potential biomarker candidates: in TCGA datasets, miR-539-5p, miR-18a-5p, and miR-130a-3p are repressed in luminal breast tumors compared to normal breast tissue, each showing moderate to good diagnostic performance (AUC ~ 0.70–0.80).ConclusionOverall, this study highlights the utility of 3D cultures in investigating the biology of breast cancer, emphasizing the critical interplay between lncRNAs, miRNAs, and mRNAs. Our findings provide insights into the discovery of novel potential biomarkers, underscoring the importance of integrating both in vitro 3D culture and in vivo expression data for a more accurate identification of miRNAs with possible applications in cancer therapies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s41065-025-00586-2.

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. In Mexico, its higher incidence and lower survival suggest a role for epigenetic factors like DNA methylation (DNAme). We conducted an epigenome-wide association study (EWAS) to define the methylation landscape and identify the profiles associated with ALL and relapse. Bone marrow or peripheral blood samples from pediatric ALL patients at diagnosis and controls without ALL were analyzed using an Infinium MethylationEPIC v2.0 array. Differential methylation was assessed using the ChAMP package. We identified a significant hypermethylated profile in ALL patients compared to controls. Probes in MAD1L1 and RPTOR contained the most differentially methylated CpG sites. Key affected pathways included proliferation, neurotransmission, and neuronal signaling. Survival analysis revealed that hypomethylation of four specific CpGs—cg01052776 (RNH1), cg20747787, cg05001671, and cg01767116 (FBXL22)—was significantly associated with an increased risk of relapse, highlighting their potential as prognostic biomarkers. This study underscores the importance of epigenetic mechanisms in pediatric ALL.

Abstract Background and Aims Autosomal dominant tubulointerstitial kidney disease (ADTKD) encompasses a group of hereditary kidney disorders characterized by tubulointerstitial fibrosis. These conditions typically follow an autosomal dominant inheritance pattern and are subclassified based on their genetic cause when identified. Pathogenic variants in UMOD, MUC1, REN, HNF1B, and SEC61A1 have been implicated in ADTKD pathogenesis. Advances in molecular diagnostics have improved genetic identification, though the true prevalence is likely underestimated. We present a cohort of ADTKD patients identified in the Nephrogenetics’ Clinic of our department between 2010 and 2024. Method Patients with chronic kidney disease (CKD) of unknown cause and undefined phenotype, or those exhibiting a renal phenotype suggestive of chronic interstitial nephritis, particularly with a family history of similar CKD, were referred to the Nephrogenetics’ Clinic for ADTKD investigation. Genetic testing methods evolved over time: Before 2015, Sanger sequencing was used. Since 2015, a stepwise genetic approach was used: (1) next-generation sequencing (NGS) for UMOD, REN, HNF1B, and SEC61A1; (2) if negative, targeted analysis for the insertion of a single cytosine in the variable-number tandem repeat (VNTR) sequence of MUC1; (3) if still negative, multiplex ligation-dependent probe amplification (MLPA) was performed to detect HNF1B deletions (P241-D2 kit, MRC-Holland). For patients with CKD and undefined phenotype, broader NGS panels for CKD were applied. Negative results underwent periodic re-evaluation, including deeper phenotyping when possible, and re-analysis using expanded gene panels, whole-exome sequencing (WES), or additional methods in reference laboratories. Pre-test genetic counseling was conducted by a nephrologist, while post-test counseling was performed jointly by a nephrologist and a geneticist, particularly for family screening and segregation studies. Results Among 35 families studied, a confirmed genetic diagnosis was obtained in 15 (43%), identifying 42 patients with ADTKD. The implicated variants were: MUC1: 5 families (18 patients); UMOD: 4 families (11 patients, all diagnosed via Sanger sequencing); HNF1B: 5 families (12 patients); REN: 1 patient with biallelic REN mutations (heterozygous). Four families presented with an undefined phenotype: two families underwent CKD panel testing due to young age at onset; two families had a cystic kidney phenotype and were tested using a cystic kidney disease panel. Notably, all these families harbored pathogenic or likely pathogenic HNF1B variants. One family underwent additional PacBio sequencing for MUC1 at a reference laboratory, leading to the identification of the dup60A variant in MUC1. Re-analysis of negative results led to the identification of pathogenic variants in two additional families: COL4A3 (heterozygous) in 1 family (2 patients); SDCCAG8 (homozygous) in 1 family (2 patients). Likely pathogenic variants were identified in: PAX2 in 1 family (3 patients); PKD1 in 1 family (3 patients); COL4A5 in 1 family (3 patients). Studies are ongoing in two families, while the remaining negative cases will undergo re-evaluation. Additionally, segregation studies are in progress for three families to assess the pathogenicity of variants in: UMOD (1 family, at least 2 patients); HNF1B (1 family, 2 patients); a family with CKD (3 patients) where the index patient carries VUS in both HNF1B and UMOD. Conclusion A genetic diagnosis of ADTKD was established in 43% of the families studied, and genetic CKD was confirmed in 57% of the families. MUC1 and UMOD were the most prevalent genes associated with ADTKD, though a significant number of cases involved HNF1B (mostly CNVs). Re-analysis of initially negative results increased the diagnostic yield for ADTKD and genetic CKD with an ADTKD-like phenotype. These findings suggest that broader gene panels as a first-line approach may enhance diagnostic accuracy. Additionally, the limitations of NGS and WES in detecting MUC1 and HNF1B variants underscore the importance of collaboration with specialized reference laboratories for ADTKD diagnosis.

Metabolic syndrome (MS) is a significant cause of morbidity and mortality worldwide, often remaining asymptomatic until complications arise. The prevalence of MS in apparently healthy populations in western Mexico is unknown. This study aimed to determine the prevalence of MS and its components in apparently healthy individuals from western Mexico. A cross-sectional study involving 947 individuals self-appointed as healthy during a screening program of MS was conducted. All participants underwent anthropometric measurements, blood pressure assessment, and laboratory tests to determine glucose, high-density lipoprotein cholesterol (HDL-C), and triglycerides levels. The diagnosis of MS was established based on the criteria outlined by the National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATPIII). Participants were categorized into three groups: healthy individuals (HS) (no components of HS), those bordering (with one or two components of MS), and those with metabolic syndrome (≥ 3 components of MS). Group comparisons were performed using ANOVA. The chi-squared test was used to assess associations between categorical variables. Student's t-test was used to compare means between the HS and MS groups. A statistical difference was considered significant when p < 0.05. The assessment identified 124 (13%) healthy individuals, 520 (55%) individuals bordering on MS, and 303 (32%) individuals with MS. The prevalence of MS was higher as age increased; women had a higher prevalence of hypoalphalipoproteinemia and elevated waist circumference, whereas men had a higher prevalence of hypertriglyceridemia. In general, men had a more impaired glycometabolic and lipidic profile. The prevalence of MS is high among self-appointed healthy individuals from Western Mexico, underscoring the need for personalized interventions focused on prevention, early detection, and treatment of MS.