Golden Helix customers are at the forefront of genetic research, using VarSeq to tackle some of the most challenging questions in genomics. From identifying novel variants to uncovering the genetic basis of rare diseases, their work showcases the power of VarSeq in real-world applications. In this blog, we’re highlighting three recent publications that demonstrate how customers are using VarSeq to make groundbreaking discoveries.
Hypohidrotic Ectodermal Dysplasia caused by an intragenic duplication in EDAR
Hypohidrotic Ectodermal Dysplasia is a syndrome with hypotrichosis, hypohidrosis, and hypodontia as the main symptoms. The prevalence is estimated to one in 5000–10,000 persons. In 10–15% the disease is caused by pathogenic variants in EDAR, and most of the known causal variants to date are missense or nonsense variants. We present a patient with classic Hypohidrotic Ectodermal Dysplasia and mammary gland aplasia with a duplication within EDAR as the likely cause. The duplication is de novo in the patient, and genome sequencing of DNA extracted from blood has revealed that the duplication is in tandem conformation, most likely entailing an altered EDAR protein with a dominant negative effect. This is, to our knowledge, the first report of an intragenic duplication in EDAR as causal for Hypohidrotic Ectodermal Dysplasia.
“The analysis was virtually focused on genes associated to ectodermal dysplasia (gene list in Supplementary Table 1) using VarSeq 2.4.0 (Golden Helix). Detection of structural variants including copy number alterations was done by the algorithms Delly, CNVnator, Lumpy og Manta.”
Duchenne Muscular Dystrophy in Two Half-Brothers Due to Inherited 306 Kb Inverted Insertion of 10p15.1 into Intron 44 of the Dp427m Transcript of the DMD Gene
Duchenne muscular dystrophy (DMD) is a rare genetic disorder caused by the absence of a fully functional dystrophin protein in myocytes. In skeletal muscle, the lack of dystrophin ultimately results in muscle wasting and the replacement of myocytes with fatty or fibrous tissues. In the heart, cardiomyocytes eventually fail and cause fatal cardiomyopathy. We present a case of a male patient and his younger brother with a maternally inherited inverted insertion of approximately 306 kb of chromosome 10 in the deep intronic region between exons 44 and 45 of the DMD gene, leading to Duchenne muscular dystrophy. Chromosomal microarray, comprehensive muscular dystrophy genetic testing, and whole exome sequencing were negative. Targeted transcriptome RNA sequencing at an external lab showed no aberrant splicing. Research whole genome sequencing identified the copy number gain and insertion. Subsequent reanalysis of the RNA sequencing data showed possible aberrant splicing involving DMD exons 44–45, and research RNA sequencing revealed a fusion between the DMD gene on the minus strand of chromosome X and the PFKFB3 gene on the plus strand of chromosome 10. We demonstrate that whole genome sequencing can be valuable for identifying intronic events in the DMD gene previously undetected or not reported by traditional clinical testing.
“HaplotypeCaller VCFs were analyzed for variants using VarSeq (Golden Helix Inc., Bozeman, MT, USA), and the Emedgene AI platform (Illumina, San Diego, CA, USA) was utilized using the HaplotypeCaller and CNVkit VCFs. VCFs from Manta were not utilized in either platform.”
MUC1-associated autosomal dominant tubulointerstitial kidney disease: prevalence in kidney failure of undetermined aetiology and clinical insights from Danish families
Abstract
Background
Frameshift variants in the variable number tandem repeat region of MUC1 cause autosomal dominant tubulointerstitial kidney disease (ADTKD-MUC1) but are challenging to detect. We investigated the prevalence in patients with kidney failure of undetermined aetiology and compared Danish families with ADTKD-MUC1.
Methods
We recruited patients with suspected kidney failure of undetermined aetiology at ≤ 50 years and excluded those with a clear-cut clinical or histopathological kidney diagnoses or established genetic kidney diseases identified thorough medical record review. MUC1 genotyping was performed by SNaPshot analysis, detecting the most common pathogenic cytosine duplication, followed by bioinformatics pipeline VNtyper analysis of short-read sequencing data..
Results
Of 172 recruited patients, 123 underwent SNaPshot analyses, which were abnormal in 5/123 patients (4%). Next, VNtyper genotyping was performed in all patients, including the five with abnormal SNaPshot analysis. VNtyper re-identified the common cytosine duplication in all five patients and revealed novel frameshift variants in two additional patients, while the analyses were normal in the remaining 116 patients. All patients carrying frameshift variants in MUC1 full-filled ADTKD criteria and had a family history of kidney failure . A considerable inter- and intra-familial variability of chronic kidney disease stage relative to age was observed in families with ADTKD-MUC1.
Conclusions
ADTKD-MUC1 was identified in 7/123 patients (6%) in a selected cohort of kidney failure of undetermined aetiology ≤ 50 years, and VNtyper effectively identified all pathogenic MUC1 variants.
“These data were also analysed for the occurrence frameshift and truncating variants in VarSeq v.2.3.0 (Golden Helix, Bozeman, MT, USA) within or outside the VNTR region, without identifying any such variants.”
Our customers continue to inspire us with their dedication to advancing genetic research. By leveraging VarSeq’s powerful capabilities, they’re breaking new ground in understanding and diagnosing complex genetic conditions. We’re proud to support their efforts and look forward to seeing what they accomplish next!