Efficient variant phasing utilizing a replication cycle reaction system

Background: Homozygous and compound heterozygous mutations in HTRA1 cause cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL). Recently, heterozygous pathogenic variants in HTRA1 were described in patients with autosomal dominant cerebral small vessel disease (CSVD). Here, we investigated the genetic variants in a cohort of Chinese patients with CSVD.Methods: A total of 95 Chinese index patients with typical characteristics of CSVD were collected. Whole exome sequencing was performed in the probands, followed by Sanger sequencing. Pathogenicity prediction software was applied to evaluate the pathogenicity of the identified variants.Results: We detected five heterozygous HTRA1 pathogenic variants in five index patients. These pathogenic variants included four known variants (c.543delT, c.854C>T, c.889G>A, and c.824C>T) and one novel variant (c.472 + 1G>A). Among them, c.854C>T, c.824C>T, and c.472 + 1G>A have never been reported in China and c.889G>A was once reported in homozygous but never in heterozygous. Three of them were distributed in exon 4, one in exon 2, and another splicing variant in intron 1. Four out of five probands presented typical features of CARASIL but less severe. The common clinical features included lacunar infarction, cognitive decline, alopecia, and spondylosis. All of them showed leukoencephalopathy, and the main involved cerebral area include periventricular and frontal area, centrum semiovale, thalamus, and corpus callosum. Anterior temporal lobes and external capsule involvement were also observed. Three probands had intracranial microbleeds.Conclusion: Our study expanded the mutation spectrum of HTRA1, especially in Chinese populations, and provided further evidence for “hot regions” in exon 1–4, especially in exon 4, in heterozygous HTRA1 pathogenic variants. Our work further supported that patients with heterozygous HTRA1 pathogenic variants presented with similar but less-severe features than CARASIL but in an autosomal dominantly inherited pattern.

BackgroundColorectal cancer (CRC) cases with an age of onset <40 years suggests a germline genetic cause. In total, 51 simplex cases were included to test the hypothesis of CRC as a mendelian trait caused by either heterozygous autosomal dominant or bi‐allelic autosomal recessive pathogenic variants.MethodsThe cohort was whole exome sequenced (WES) at 100× coverage. Both a dominant‐ and recessive model were used for searching predisposing genetic factors. In addition, we assayed recessive variants of potential moderate risk that were enriched in our young‐onset CRC cohort. Variants were filtered using a candidate cancer gene list or by selecting variants more likely to be pathogenic based on variant type (e.g., loss‐of‐function) or allele frequency.ResultsWe identified one pathogenic variant in PTEN in a patient subsequently confirmed to have a hereditary hamartoma tumor syndrome (Cowden syndrome) and one patient with a pathogenic heterozygous variant in PMS2 that was originally not identified by WES due to low quality reads resulting from pseudogenes. In addition, we identified three heterozygous candidate missense variants in known cancer susceptibility genes (BMPR1A,BRIP1, and SRC), three truncating variants in possibly novel cancer genes (CLSPN,SEC24B, SSH2) and four candidate missense variants in ACACA, NR2C2, INPP4A, and DIDO1. We also identify five possible autosomal recessive candidate genes: ATP10B,PKHD1,UGGT2,MYH13,TFF3.ConclusionTwo clear pathogenic variants were identified in patients that had not been identified clinically. Thus, the chance of detecting a hereditary cancer syndrome in patients with CRC at young age but without family history is 2/51 (4%) and therefore the clinical benefit of genetic testing in this patient group is low. Of note, using stringent filtering, we have identified a total of ten candidate heterozygous variants and five possibly biallelic autosomal recessive candidate genes that warrant further study.

A case report of riboflavin transporter deficiency: A novel heterozygous pathogenic variant in the SLC52A3 gene

BackgroundHomozygous or compound heterozygous pathogenic variants in the thromboxane A synthase 1 (TBXAS1) gene are associated with Ghosal hematodiaphyseal dysplasia (GHDD) which is characterized by defective hematopoiesis and increased bone density of long bones.MethodsPatients 1 and 2 are identical twins, who presented with red blood cell transfusion‐dependent normocytic anemia and thrombocytopenia with bone marrow fibrosis and cortical bone thickening of long bones on plain radiograph. To clarify the etiology of their anemia and thrombocytopenia, whole blood was used for the DNA extraction and analyzed using next‐generation sequencing (NGS) on an in‐house bone marrow failure syndrome panel.ResultsThe NGS results indicated that these two patients carried two heterozygous variants in TBXAS1, exon7, c.583_584del, p.Ala195Leufs*12, and exon12, c.1420G>T, p.Gly474Trp, which were inherited from their mother and father, respectively. Patients 1 and 2 have been on chronic oral steroids with normalization of hemoglobin and platelet count after steroid initiation. Patient 3 is their sister who has normal blood counts but also has the same variants in TBXAS1 as her brothers. Radiographs showed cortical bone thickening and she has not required any treatment or transfusion.ConclusionWe report three Caucasian siblings from non‐consanguineous parents with novel compound heterozygous variants of TBXAS1 presenting with the phenotypes of GHDD. These three cases illustrate the variable clinical expressivity of the GHDD from two‐compound heterozygous pathogenic variants of TBXAS1.

Familial dementia is a rare inherited disease involving progressive impairment of memory, thinking, and behavior. We report a novel heterozygous pathogenic variant (c.199G > A, p.Val67Ile) in the CIAO1 gene that appears to be co-segregated with Alzheimer’s disease in a Japanese family. Biochemical analysis of CIAO1 protein revealed that the variant increases the interaction of CIAO1 with immature amyloid-β protein precursor (AβPP), but not mature or soluble AβPP, indicating plausible CIAO1 involvement in AβPP processing. Our study indicates that a heterozygous variant in the CIAO1 gene may be closely related to autosomal dominant familial dementia.

Two rare loss-of-function variants in the STAG3 gene leading to primary ovarian insufficiency

ObjectiveThe detection and monitoring of DNA methylation status in circulating tumor cell DNA (ctDNA) provides critical insights into cancer diagnosis and progression. The methylation status of the Dickkopf-related protein 3 (DKK3) promoter region is correlated with the metastasis and recurrence of multiple cancers. Thus, detecting the methylation status via non-invasive methods is essential for the diagnosis and prognosis of cancers. Using a droplet digital polymerase chain reaction approach, we have developed a highly sensitive and quantitative measurement of methylated and unmethylated DKK3 derived from circulating cell-free DNA (ccfDNA).ResultsWe confirmed the specificity of droplet digital methylation specific polymerase chain reaction (ddMSP). We selected the optimal bisulfite conversion method using commercially available kits. We validated the ddMSP analysis system by analyzing the methylation status of genomic DNA extracted from cultured mesothelioma cells and mesothelial cells. Our system quantified approximately 30 copies of cell-free DNA per 4 mL, which is sufficient for detecting ctDNA. Finally, we quantified methylated and unmethylated DKK3 copies in ccfDNA from 21 patients with malignant mesothelioma.

Heterozygous pathogenic variants in the histidyl‐tRNA synthetase (HARS) gene are associated with Charcot–Marie–Tooth (CMT) type 2W disease, classified as an axonal peripheral neuropathy. To date, at least 60 variants causing CMT symptoms have been identified in seven different aminoacyl‐tRNA synthetases, with eight being found in the catalytic domain of HARS. The genetic data clearly show a causative role of aminoacyl‐tRNA synthetases in CMT; however, the cellular mechanisms leading to pathology can vary widely and are unknown in the case of most identified variants. Here we describe a novel HARS variant, c.412T>C; p.Y138H, identified through a CMT gene panel in a patient with peripheral neuropathy. To determine the effect of p.Y138H we employed a humanized HARS yeast model and recombinant protein biochemistry, which identified a deficiency in protein dimerization and a growth defect which shows mild but significant improvement with histidine supplementation. This raises the potential for a clinical trial of histidine.

Objective: Neurodevelopmental disorder with or without seizure and gait abnormalities (NEDSGA, MIM * 617864) is a newly described autosomal dominant inherited disease caused by a heterozygous variant in the GRIA4 gene. GRIA4 plays an essential role in excitatory synaptic transmission. In this study, we presented the clinical and genetic features of a female patient carrying a novel de novo variant in GRIA4 and further reviewed the previously reported five different patients.Methods: Evaluation of the patient included a detailed history and clinical examination. Trio-whole exome sequencing (WES) was performed to identify pathogenic variants in NEDSGA. Sanger sequencing was further used to validate the variants.Results: We described the clinical features of an infant diagnosed with NEDSGA caused by a GRIA4 variant, who presented with severe developmental delay, limb hypertonia, generalized seizure, retinal hypoplasia, and chorioretinal hyperpigmentation. The patient developed tricuspid regurgitation, and imaging examination revealed a patent foramen ovale. Trio-WES identified a novel de novo heterozygous missense variant c.1918G>T, p.Ala640Ser in the GRIA4 gene. Multiple in silico tools predicted deleterious effects of p.Ala640Ser.Conclusion: A novel heterozygous missense variant in the GRIA4 gene (c.1918G>T) identified in the proband expanded the genotypic and phenotypic spectrum of disorders associated with GRIA4 variants. This is the first NEDSGA case reported in China. Our findings provide valuable information for the differential diagnosis of neonatal onset neurodevelopmental disorders.

BackgroundCongenital hydrocephalus‐3 with brain anomalies (HYC3, MIM 617967) is a rare form of congenital hydrocephalus characterized by severe hydrocephalus and cerebellar abnormalities, the onset of the disease occurs in utero even resulting in fetal death. A very limited spectrum of WDR81 pathogenic variants had been reported in three unrelated families with HYC3. This study aims at presenting novel compound heterozygous frameshift variants in WDR81 in a Chinese fetus.MethodsWhole‐exome sequencing (WES) was performed for a fetus with multiple congenital anomalies including sever hydrocephalus, cleft lip and palate, hydrops fetalis, hepatomegaly, and cerebellar hypoplasia. Sanger sequencing was performed to confirm the origin of the variants subsequently. Variants classification was based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines.ResultsTwo novel heterozygous variants c.146_147insG (p.Thr52fs) and c.673delC (p.Leu225fs) in WDR81 were identified. Sanger sequencing revealed that the c.146_147insG mutation was maternal origin and the c.673delC mutation was paternal origin. Both variants were pathogenic according to the ACMG/AMP guidelines.ConclusionThe present study expands the mutation spectrum of WDR81 and help further define the genotype–phenotype correlations of HYC3. WDR81‐related HYC3 were highly clinical heterogeneity. We suggested that fetal hydrocephalus with extracerebral manifestations may be suggestive of WDR81 deficiency and WES is effective for achieving a conclusive diagnosis for disorder.

A Novel Heterozygous TGFBI c.1613C>A Pathogenic Variant is Associated With Lattice Corneal Dystrophy in a Chinese Family

Retinitis pigmentosa (RP) is the most common and highly heterogeneous form of hereditary retinal degeneration. This study was to identify mutations in the 60 genes that were known to be associated with RP in 157 unrelated Chinese families with RP. Genomic DNA from probands was initially analyzed by whole exome sequencing. Sanger sequencing was used to confirm potential candidate variants affecting the encoded residues in the 60 genes, including heterozygous variants from genes that are related to autosomal dominant RP, homozygous or compound heterozygous variants from genes that are related to autosomal recessive RP, and hemizygous variants from genes that are related to X-linked RP. Synonymous and intronic variants were also examined to confirm whether they could affect splicing. A total of 244 candidate variants were detected by exome sequencing. Sanger sequencing confirmed 240 variants out of the 244 candidates. Informatics and segregation analyses suggested 110 potential pathogenic mutations in 28 out of the 60 genes involving 79 of the 157 (50%) families, including 31 (39%, 31/79) families with heterozygous mutations in autosomal dominant genes, 37 (47%, 37/79) families with homozygous (9) or compound heterozygous (28) mutations in autosomal recessive genes, and 11 (14%, 11/79) families with hemizygous mutations in X-linked genes. Of the 110 identified variants, 74 (67%) were novel. The genetic defects in approximately half of the 157 studies families were detected by exome sequencing. A comprehensive analysis of the 60 known genes not only expanded the mutation spectrum and frequency of the 60 genes in Chinese patients with RP, but also provided an overview of the molecular etiology of RP in Chinese patients. The analysis of the known genes also supplied the foundation and clues for discovering novel causative RP genes.

Introduction: Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, B-cell lymphoma with highly prevalent somatic mutations including MYD88, and CXCR4. The mutation rates of LPL/WM in China and the direct comparison among different deletion means are still not clear. Methods: 387 patients with LPL/WM were included in this study. Tumor cells were collected from 357 un-sorted BM 28 PB and 2 lymph nodes (FFPE). MYD88L265P mutation were detected by Sanger sequencing (FGS), NGS, allele-specific quantitative polymerase chain reaction (ASPCR), and droplet digital polymerase chain reaction (ddPCR). CXCR4 mutation were detected by Sanger sequencing, NGS, and ASPCR. Results: 386 patients were assessed for MYD88L265P mutation, of whom 263 were tested by FGS, 235 by NGS, 311 for AS-PCR, 118 for ddPCR. The MYD88L265P mutation was found in 88.6% of the patients. ASPCR and ddPCR had the highest sensitivity of 97.1% and 96.8%. FGS and NGS failed to detected the mutation in low tumor load. A high false-negative rate (FNR) for MYD88 by FGS and NGS was observed in patients with tumor load less than 10% (FNR: 35.5% and 20%). There was no significant difference in the MYD88 mutation rate detected by ddPCR and ASPCR among patients with different tumor load groups (p = 0.794). MYD88 mutation was detected in a high incidence of 88.5% in less than 1% infiltrated WM tumor cells specimens by ddPCR and ASPCR. CXCR4 mutation testing was performed in 358 patients of LPL/WM, comprising 301 with FGS, 236 with NGS, and 311 with ASPCR. Overall, 31.2% patients were identified as having the CXCR4 mutation. NGS exhibited the highest sensitivity among the three detection means. MYD88 wild-type patients had a significantly lower Hb levels (median 79 g/L vs. 90 g/L, p = 0.015), lower proportion of males (54.5% vs. 51.8%, p = 0.012) and a significantly higher proportion elevated β2-MG (84.2% vs. 65.6%, p = 0.021), and LDH (30.2% vs. 11.9%, p = 0.001). However, there were no significant differences in either PFS or OS between MYD88L265P wild-type and MYD88L265P mutation group (p = 0.35, p = 0.42). Patients with CXCR4 mutation tended to be older (median 64 vs. 60, p < 0.001) and displayed lower hemoglobin level (median 81 g/L vs. 93 g/L, p = 0.008), higher serum IgM level (median 36.1 g/L vs. 31.6 g/L, p < 0.001), and higher baseline BM involvement (by FCM, median 15.1% vs. 7.1%, p < 0.001) compared with CXCR4 wild-type patients. Notably, CXCR4 mutation group had significantly worse survival compared with the wild-type group (p = 0.03, p = 0.02). The research was funded by: National Nature Science Foundation of China (81970187, 82170193, 81920108006, and 81900203) and the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (2022-I2M-1-022, 2021-I2M-C&T-B-081) Keywords: diagnostic and prognostic biomarkers, indolent non-Hodgkin lymphoma No conflicts of interests pertinent to the abstract.

Whole exome sequencing (WES) has become an increasingly common technique for identifying the genetic cause of Mendelian genetic diseases. However, it may fail to detect the complex regions of the genome. Here, we investigated the genetic etiology of a pedigree with autosomal dominant polycystic kidney disease (ADPKD) using a combination of WES, multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, and long-read sequencing (LRS). Initially, WES of the proband revealed a heterozygous variant c.7391G>C in PKD1 Exon 18, along with a heterozygous deletion of the 17th and 18th exons of PKD1 detected by exome-based copy number variation (CNV) analysis. MLPA confirmed the PKD1 heterozygous deletion of Exon 18. Except for c.7391G>C, Sanger sequencing identified four other heterozygous variants (c.7278T>C, c.7288C>T, c.7344C>G, and c.7365C>T) in Exon 18 of PKD1. Subsequently, LRS uncovered seven clustered substitution variants (c.7209+28C>T, c.7210-16C>T, c.7278T>C, c.7288C>T, c.7344C>G, c.7365C>T, and c.7391G>C), with six of them omitted by WES due to interference from PKD1 pseudogenes. Combining LRS results with cosegregation of the pedigree analysis, we found these variants were in cis and converted from PKD1 pseudogenes, covering a region of at least 282 bp. Notably, the paralogous sequence variants of c.7288C>T introduced a premature stop codon of PKD1, leading to a function loss, and were classified as pathogenic (PVS1+PS4+PM2) according to the ACMG/AMP guideline. Our study highlights the limitations of WES/MLPA and the importance of utilizing complementary tools like LRS for comprehensive variant detection in PKD1.

Patients with non-small cell lung cancer (NSCLC) commonly harbor epidermal growth factor receptor (EGFR) mutation. Due to the complex disease pathology, early-stage diagnosis of patients with EGFR mutation is essential to make appropriate treatment decision. Tyrosine kinase inhibitors (TKIs) are commonly used for their treatment, but almost half of the patients with EGFR mutation do not respond to the available TKIs and develop acquired resistance owing to T790M mutation. The presence of T790M mutation also warrants a robust diagnostic method so as to allow clinicians to modify cancer treatment. Numerous diagnostic techniques for the detection of EGFR mutation, however, their performance and working profile variation necessitate a comparative evaluation for the selection of a better diagnostic method or an advanced combination of theirs. The present review compares various EGFR-mutation detection techniques such as Sanger sequencing, next-generation sequencing, and different polymerase chain reaction (PCR)-based methods. It also highlights the role of advanced PCR-based techniques, i.e., real-time or quantitative PCR and digital droplet PCR (ddPCR) for detecting EGFR mutations in NSCLC patients. ddPCR, when compared to other methods, shows enhanced sensitivity, superior reliability, and improved time and cost-effectiveness. Moreover, its ability to detect EGFR mutations including T790M, in both conventional (solid tissue biopsy samples) and nonconventional sample sources (blood, plasma, and urine samples), gives it an edge over other diagnostic techniques and support its integration in clinical practice setting.