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Introduction A robust genetic test for BRCA1 and BRCA2 genes is necessary for the diagnosis, prognosis, and treatment of patients with hereditary breast and ovarian cancer. We evaluated a commercial amplicon-based massively parallel sequencing (MPS) assay, BRCA MASTR Plus on the MiSeq platform, for germline BRCA genetic testing. Methods This study was performed on 31 DNA from cell lines and proficiency testing samples to establish the accuracy of the assay. A reference cell line DNA, NA12878 was used to determine the reproducibility of the assay. Discordant MPS result was resolved orthogonally by the current gold-standard Sanger sequencing method. Results The analytical accuracy, sensitivity, and specificity for variant detection were 93.55, 92.86, and 100.00%, respectively. Both sequencing depth and variant allele frequencies were highly reproducible by comparing the NA12878 DNA tested in three separate runs. The single discordant result, later confirmed by Sanger sequencing was due to the inability of the MASTR Reporter software to identify a 40-bp deletion in BRCA1. Conclusion The BRCA MASTR Plus assay on the MiSeq platform is accurate and reproducible for germline BRCA genetic testing, making it suitable for use in a clinical diagnostic laboratory. However, Sanger sequencing may still serve as a confirmatory method to improve diagnostic capability of the MPS assay.

An infant with 46,XY karyotype, and unambiguous female phenotype was found to have testes in the inguinal regions. Capillary sequencing of the androgen receptor (AR) gene identified a hemizygous de novo mutation (NM_000044.6:c.1621G > T) in exon 2 resulting in a termination codon p.(Glu541*) at the DNA binding domain (DBD). This novel nonsense mutation adds to the compendium of AR mutations which result in complete androgen insensitivity syndrome (AIS).

Aim: Two missense variants in the HFE gene, c.845G>A (p.Cys282Tyr) and c.187C>G (p.His63Asp), are commonly screened as part of the diagnostic workup for HFE-related hereditary hemochromatosis (HH) ...

Multinational studies have reported monogenic etiologies in 25%-30% of children with steroid-resistant nephrotic syndrome. Such large studies are lacking in Asia. We established Deciphering Diversities: Renal Asian Genetics Network (DRAGoN) and aimed to describe the genetic and clinical spectrums in Asians. We prospectively studied a cohort of 183 probands with suspected genetic glomerulopathies from South and Southeast Asia, of whom 17% had positive family history. Using multi-gene panel sequencing, we detected pathogenic variants in 26 (14%) probands, of whom one-third had COL4A4 or COL4A5 variants (n = 9, 5%). Of those with COL4A5 defects, only 25% had features suggestive of Alport syndrome. Besides traditional predictors for genetic disease (positive family history and extrarenal malformations), we identified novel predictors, namely older age (6.2 vs. 2.4 years; p = 0.001), hematuria (OR 5.6; 95% CI 2.1-14.8; p 0.001), and proteinuria in the absence of nephrotic syndrome (OR 4.6; 95% CI 1.8-11.8; p = 0.001) at first manifestation. Among patients who first presented with proteinuria without nephrotic syndrome, the genetic diagnostic rates were60% when a second risk factor (positive family history or extrarenal manifestation) co-existed. The genetic spectrum of glomerulopathies appears different in Asia. Collagen IV genes may be included in sequencing panels even when suggestive clinical features are absent.

Objective The nucleoside diphosphate linked moiety X (Nudix)-Type motif 15 (NUDT15) enzyme is involved in thiopurine metabolism. Genetic variants in the NUDT15 gene result in decreased NUDT15 activity, which in addition to decreased thiopurine S-methyltransferase (TPMT) activity, contributes to thiopurine toxicity. Current standard approaches of NUDT15 genetic analysis have mainly been targeting several common variants. We aimed to develop a clinical-grade DNA-based assay for genetic analysis of the NUDT15 gene using Sanger di-deoxy sequencing. Results Sanger sequencing results were fully concordant with the expected NUDT15 genotype in all 17 cell line samples with known NUDT15 variants (accuracy = 100%; 95% CI 80.49 to 100.00%). Precision studies showed 100% intra-run repeatability and 100% inter-run reproducibility, respectively. Genetic analysis of the NUDT15 gene was performed for 80 patients of Asian ethnicity with wildtype TPMT. 76% (N = 61) of the studied individuals had NUDT15 *1/*1 diplotype. 25% (N = 14) of Chinese and 36% (N = 5) of Malays were found to carry at least 1 non-functional NUDT15 allele. Our study confirmed a high frequency of NUDT15 c.415C>T and c.55_56insGAGTCG variants in the Chinese and Malay ethnic groups in Singapore, highlighting the importance of determining NUDT15 genotype prior to thiopurine dosing.

Pathogenic variants in the PHEX gene are causative of X-linked hypophosphatemic rickets (XLH). We present a case of a 2-year-old girl with hypophosphatemic rickets with genu varum and short stature without any family history of XLH. Next generation sequencing of the PHEX gene identified a splice donor variant, NM_000444.6:c.1173 + 5G > A in intron 10. This variant had a mosaic pattern with only 22% of the sequence reads showing the variant allele and was not present in the girl's parents, both of whom had a normal phenotype. This is a sporadic case of a de novo mosaic splice-site variant in the PHEX gene.

The liver X receptor (LXR) is a key transcriptional regulator of cholesterol, fatty acid, and phospholipid metabolism. Dynamic remodeling of immunometabolic pathways, including lipid metabolism, is a crucial step in T cell activation. Here, we explored the role of LXR-regulated metabolic processes in primary human CD4(+) T cells and their role in controlling plasma membrane lipids (glycosphingolipids and cholesterol), which strongly influence T cell immune signaling and function. Crucially, we identified the glycosphingolipid biosynthesis enzyme glucosylceramide synthase as a direct transcriptional LXR target. LXR activation by agonist GW3965 or endogenous oxysterol ligands significantly altered the glycosphingolipid:cholesterol balance in the plasma membrane by increasing glycosphingolipid levels and reducing cholesterol. Consequently, LXR activation lowered plasma membrane lipid order (stability), and an LXR antagonist could block this effect. LXR stimulation also reduced lipid order at the immune synapse and accelerated activation of proximal T cell signaling molecules. Ultimately, LXR activation dampened proinflammatory T cell function. Finally, compared with responder T cells, regulatory T cells had a distinct pattern of LXR target gene expression corresponding to reduced lipid order. This suggests LXR-driven lipid metabolism could contribute to functional specialization of these T cell subsets. Overall, we report a mode of action for LXR in T cells involving the regulation of glycosphingolipid and cholesterol metabolism and demonstrate its relevance in modulating T cell function.

Beta thalassaemia is one of the most common heritable haematological disorders worldwide. Although beta thalassaemia has an autosomal recessive mode of inheritance, the clinical presentations can be classified according to different categories of severity aligning to zygosity of the affected Beta Globin ( HBB ) gene and the effects of the pathogenic variants to beta globin chain production. Most of the beta globin variants have been named after the alphabets, geographical regions and HBB gene codons. Such ‘legacy’ tradition has also been commonly practised in naming alpha globin variants. Being the most studied gene in the human genome by the mid-1980s,1 the HBB gene is one of the earliest annotated genes. Located at 11p15.5,2 the HBB has three exons encoding 147 amino acids. The promoter and 5′ untranslated region (UTR) have multiple binding sites for transcriptional factors. The 3′ UTR contains a site of polyadenylation signal which is important for mRNA cleavage and RNA stability. Mutational spectrum of the HBB gene is highly heterogeneous, including mostly single-base substitutions, small insertions or deletions of one or a few bases in the gene sequences with functional importance. Many pathogenic variants reported in the intronic regions are known to and could potentially activate cryptic splice-sites affecting the transcribed mRNAs. The current standard genomic and mRNA reference sequences are NG\_059281.1 and NM\_000518.5, respectively. We read with great interest the article by Zhuang …

Glucokinase-maturity-onset diabetes of the young (GCK-MODY or MODY 2), caused by a heterozygous inactivating variant in the Glucokinase (GCK) gene, is a common form of MODY. Here, we present a case of GCK-MODY in a young Chinese boy, his sister and his father with a novel pathogenic variant in exon 8 of the GCK gene, NM_000162.5:c.1015del, p.(Glu339Argfs*14), which is predicted to cause a significant change in protein structure and function.

The Cepheid Xpert® Norovirus kit automates sample processing, nucleic acid extraction, and real-time reverse transcription polymerase chain reactions (RT-PCRs) to detect norovirus genogroups I (GI) and II (GII). Eighty-five stool samples collected between February 2015 and May 2017 were used to compare the performance of a user-modified Xpert assay against a clinically validated laboratory-developed test (LDT). Of the 85 samples, 54 were previously archived in -80°C freezer. The remaining 31 were fresh samples tested concurrently with the LDT. The results of all samples tested using the Xpert kit and LDT were found to be concordant, including 12 GI- and 42 GII-positive samples, 1 GI and GII coinfection, and 30 negative samples. Comparison of the assays showed perfect concordance with a kappa coefficient score of 1.00 (95%CI from 1.00 to 1.00). Of the 30 negative stool samples tested, three samples were positive for rotavirus detected using an immunochromatographic assay, with no cross-reactivity shown in both LDT and Xpert assays. In-run sample processing control of the Xpert assay for all negative samples tested showed no/minor inhibition. Compared to the LDT, the Xpert assay produced similar or better Ct values for detection. It also showed better mitigation of PCR inhibition in stool sample testing.

The liver X receptor (LXR) is a key transcriptional regulator of cholesterol, fatty acid, and phospholipid metabolism. Dynamic remodeling of immunometabolic pathways, including lipid metabolism, is a crucial step in T cell activation. Here we explored the role of LXR-regulated metabolic processes in primary human CD4+ T cells, and their role in controlling plasma membrane lipids (glycosphingolipids and cholesterol) which strongly influence T cell immune signaling and function. Crucially, we identified the glycosphingolipid biosynthesis enzyme glucosylceramide synthase (UGCG) as a direct transcriptional LXR target. LXR activation by agonist GW3965 or endogenous oxysterol ligands significantly altered the glycosphingolipid:cholesterol balance in the plasma membrane by increasing glycosphingolipid levels and reducing cholesterol. Consequently, LXR activation lowered plasma membrane lipid order (stability), and an LXR antagonist could block this effect. LXR stimulation also reduced lipid order at the immune synapse and accelerated activation of proximal T cell signaling molecules. Ultimately, LXR activation dampened pro-inflammatory T cell function. Finally, compared to responder T cells, regulatory T cells had a distinct pattern of LXR-target gene expression corresponding to reduced lipid order. This suggests LXR-driven lipid metabolism could contribute to functional specialization of these T cell subsets. Overall, we report a novel mode of action for LXR in T cells involving the regulation of glycosphingolipid and cholesterol metabolism, and demonstrate its relevance in modulating T cell function.

Wilson disease (WD), a disorder of copper metabolism resulting in copper accumulation in the liver and other organs, is an inherited autosomal recessive genetic condition.1 Diagnosis is challenging and is based on clinical symptoms (neuropsychiatric or hepatic dysfunction), clinical signs (presence of Kayser-Fleischer (KF) rings) and laboratory test results (abnormal liver function tests, low serum caeruloplasmin and elevated urinary copper excretion).2 However, the biochemical findings may be inconclusive as concentrations of serum caeruloplasmin and urinary copper in patients with WD can overlap with those of healthy individuals.2 To try to overcome such issues, laboratory-derived indices have been suggested, such as non-caeruloplasmin bound copper, percentage non-caeruloplasmin bound copper, copper caeruloplasmin ratio and copper adjusted for caeruloplasmin, but the reference ranges and cut-offs differ between laboratories.3–6 In addition, scoring systems exist,7 some of which may incorporate genetic testing.8 Molecular diagnostic testing is performed to confirm or exclude the diagnosis in patients with symptoms and biochemical findings suggestive of WD.2 7 ### Sequencing the ATP7B gene Genetic testing of WD is performed by screening for loss-of-function variants in the ATP7B gene. Diagnostic confirmation can be achieved by identifying two pathogenic variants in the compound heterozygous state or a single pathogenic variant in the homozygous state. More than 500 WD-causing variants in the ATP7B gene including single nucleotide variants, small deletions and insertions have been reported in literature and public databases such as ClinVar, Leiden Open Variation Database, Human Genetic Variation Database and the Wilson Disease Mutation Database.9 Although the gene harbours several population-specific variants, many pathogenic variants throughout the entire gene have been found to be rare and only familial-specific.10 Therefore, screening tests that contain only specific, most frequent variants, although not as labour-intensive and time-consuming as whole gene screening, may miss rare pathogenic variants. Sanger sequencing is currently …

Objectives In recent years, next-generation sequencing (NGS) technologies, which enable high throughput sample processing at relatively lower costs, are adopted in both research and clinical settings. A multiplex PCR-based NGS assay to identify mutations in the ATP7B gene for routine molecular diagnosis of Wilson disease was evaluated in comparison with the gold standard direct Sanger sequencing. Design and methods Five multiplex PCRs to amplify the partial promoter, 5′ untranslated and the entire coding regions of the ATP7B gene were designed. Indexed paired-end libraries were generated from the pooled amplicons using Nextera XT DNA Sample Preparation Kit and subjected to NGS on the MiSeq platform. DNA from the peripheral blood of 12 patients with Wilson disease, 2 B-lymphocyte cell lines and 3 external quality assurance samples were sequenced by the MiSeq and Sanger sequencing. Results Complete coverage was achieved across the targeted bases without any drop-out sequences. The observed read depth in a single run with 20 samples was > 100X. Comparison of the NGS results against Sanger sequencing data on a panel of clinical specimens, cell lines and European Molecular Genetics Quality Networks (EMQN) quality assurance samples showed 100% concordance in identifying pathogenic mutations. Conclusion With the capability of generating relatively higher throughput in a short time period, the NGS assay is a viable alternative to Sanger sequencing for detecting ATP7B mutations causally linked to Wilson disease in the clinical diagnostic laboratory.

Diagnosis and classification of poorly differentiated tumors with primitive features of the central nervous system heavily relies on molecular and genetic findings of the tumors. Although RB1 gene mutation underlies the development of retinoblastoma and many other systemic cancers, RB1 gene mutation in a brain tumor is mainly limited to infiltrating gliomas. We describe what we believe to be a hitherto unreported case of sellar/suprasellar embryonal tumor with distinctive Flexner-Wintersteiner rosette formation, and somatic RB1 gene mutation in a 5-month-old infant. There were no molecular features associated with the embryonal tumor with multi-layered rosettes, and there were no histological or genetic features of a germ cell tumor. A follow up of 14 months duration showed good clinical response to VETOPEC regimen and no development of retinal disease. Our case shows an interesting association between RB1 mutation and Flexner-Wintersteiner rosettes in an embryonal tumor of the central nervous system and underscores the utility of large scale next generation sequencing in helping to identify the genetic aberrations that may help in clinical pathologic correlations of unusual or out-of-place histologic findings.

The aim of our study was to establish an unlabeled probe genotyping approach for rapid detection of the MYD88 L265P mutation in the differential diagnosis of Waldenstrӧm macroglobulinemia patients. Analytical and clinical validation of the assay was performed using serially diluted amplicon-cloned standards, 14 clinical bone marrow aspirate samples, and 30 peripheral blood samples from healthy donors, respectively. The analytical validation results showed that the assay is able to reproducibly identify as low as 10% of the L265P mutant. Clinical validation results showed improved detection sensitivity for the L265P mutation compared to Sanger sequencing. With the simplicity, cost-effectiveness, specificity and rapidity, we foresee that the unlabeled probe HRM assay is a good alternative to substitute current established methods for routine diagnostic testing of the MYD88 L265P mutation.

A 64-year-old man presented with gastrointestinal bleeding and inguinal lymphadenopathy. His lymph node biopsy is presented in slide A. An IgM paraprotein was detected in his serum while a full blood count and film suggested iron deficiency with no lymphocytosis. A small bowel mass was detected on CT scan but the patient declined further investigations including bone marrow studies. He was treated based on the lymph node histology with transient resolution of the bleeding. He subsequently underwent resection of the small bowel mass due to recurrent bleeding. The histology of the small bowel mass is presented in slide B. Review the high-quality, interactive digital Aperio slide at http://virtualacp.com/JCPCases/jclinpath-2017-204415\_A/ and http://virtualacp.com/JCPCases/jclinpath-2017-204415\_B/ …

A rapid, duplex, high-resolution melting interleukin-28B gene ( IL28B ) genotyping assay, targeting both rs12979860 and rs8099917 polymorphisms, was developed and validated using 30 DNA samples from healthy volunteers. A linkage study on 300 healthy Singaporeans showed variable haplotypes. When the assay was applied to plasma DNA from 50 hepatitis C virus genotype-1 (HCV-1)-infected patients, five compound heterozygous types were detected.

Loss-of-function mutations in the phosphate regulating gene with homologies to endopeptidases on the X-chromosome ( PHEX) have been causally associated with X-linked hypophosphatemic rickets (XLHR). The early diagnosis of XLHR in infants is challenging when it is based solely on clinical features and biochemical findings. We report a 7-month-old boy with a family history of hypophosphatemic rickets., who demonstrated early clinical evidence of rickets, although serial biochemical findings could not definitively confirm rickets. A sequencing assay targeting the PHEX gene was first performed on the mother’s DNA to screen for mutations in the 5′UTR, 22 coding exons, and the exon-intron junctions. Targeted mutation analysis and mRNA studies were subsequently performed on the boys’ DNA to investigate the pathogenicity of the identified mutation. Genetic screening of the PHEX gene revealed a novel mutation, c.1080-2A>C, at the splice acceptor site in intron 9. The detection of an aberrant mRNA transcript with skipped (loss of) exon 10 establishes its pathogenicity and confirms the diagnosis of XLHR in this infant. Genetic testing of the PHEX gene resulted in early diagnosis of XLHR, thus enabling initiation of therapy and prevention of progressive rachitic changes in the infant.