OBJECTIVES:To investigate the association between insulin resistance and uterine volume in girls with idiopathic central precocious puberty (ICPP). METHODS:A retrospective study was conducted involving 61 girls diagnosed with ICPP who visited the pediatric growth and development clinic of the Third Affiliated Hospital of Zhengzhou University between January 2022 and September 2024, designated as the ICPP group, and 61 normally developing girls as the control group. The differences in insulin resistance index (homeostasis model assessment of insulin resistance, HOMA-IR), uterine volume, and other indicators between the two groups were compared, and the relationship between insulin resistance and uterine volume in these girls was analyzed. RESULTS:The uterine volume and HOMA-IR level in the ICPP group were significantly higher than those in the control group (P<0.05). Correlation analysis revealed that there was a positive correlation between HOMA-IR level and uterine volume in the ICPP group (rs=0.643, P<0.001). Multiple linear regression analysis indicated that as HOMA-IR increased,uterine volume in the girls tended to increase (P<0.05). CONCLUSIONS:There is an association between insulin resistance and uterine volume in girls with ICPP, and as HOMA-IR increases, uterine volume in the girls also increases.

Background:17α-hydroxylase deficiency (17-OHD) represents the rarest subtype of congenital adrenal hyperplasia (CAH), characterized by impaired cortisol and sex hormone synthesis due to CYP17A1 enzyme deficiency. The classic clinical triad includes hypokalemia, drug-resistant hypertension, and sexual infantilism. The lack of prominent prepubertal sexual development characteristics may lead to delayed diagnosis of 17-OHD. This study completely documents a prepubertal child with 17-OHD, characterized by recurrent hypertension, hypokalemia, and respiratory infections, encompassing the entire course from clinical discovery, genetic diagnosis, treatment initiation, to 24-month follow-up. Case Description:A 10-year-old girl presented with recurrent hypokalemia, hypertension, and respiratory tract infections. Hormonal testing revealed pathognomonic features of 17-OHD, including elevated progesterone, undetectable cortisol, suppressed renin activity, elevated mineralocorticoid precursors, and reduced sex hormones. Genetic analysis confirmed CYP17A1 compound heterozygous variants: a novel pathogenic mutation (c.1082T>C: p.L361P), rare exome variant ensemble learner (REVEL) score 0.94, and a known frameshift mutation (c.985_987delinsAA: p. Y329Kfs90), with concurrent 15q11.2 microdeletion. The treatment plan included hydrocortisone, metoprolol, captopril, and potassium supplementation to stabilise blood pressure and serum potassium levels. At the 24-month follow-up, new-onset arrhythmias and non-autoimmune thyroid dysfunction were documented. Conclusions:17-OHD can present with recurrent hypokalemia, refractory hypertension, and respiratory tract infections in childhood, which are prone to misdiagnosis. Early hormonal testing (such as elevated progesterone and decreased cortisol) and CYP17A1 gene analysis are crucial for diagnosis, and the discovery of the novel mutation (c.1082T>C: p.L361P) enriches its genetic spectrum.

The global burden of non-alcoholic steatohepatitis (NASH) is on the rise. Researchers recognize inhibiting ferroptosis, a form of cell death leading to iron-dependent oxidative damage, as a promising therapy for treating NASH. Lycopene, a natural antioxidant compound, exhibits various pharmacological properties. However, the anti-NASH efficacy of the dietary recommended concentration of lycopene and the role of lycopene in combating ferroptosis in NASH have remained unclear. Our study investigated lycopeneu2019s impact on ferroptosis in various diet-induced mouse NASH models and corresponding cellular models, unveiling its anti-inflammatory and anti-fibrotic effects. Our findings demonstrated that lycopene notably reduced ferroptosis in methionine- and choline-deficient (MCD) diet-fed mice and a normal mouse hepatocyte cell line (NCTC1469) by restoring balanced ferrous iron levels, lipid reactive oxygen species, and normal mitochondrial morphology. These effects were linked to the regulation of ferroptosis markers glutathione peroxidase 4 (GPX4) and prostaglandin G/H synthase 2. Additionally, lycopeneu2019s anti-ferroptosis action was validated in mice fed a high-fat, high-cholesterol diet and HepG2 cells treated with free fatty acid. Our transcriptomic analysis highlighted peroxisome proliferator-activated receptor u03B1 (PPARu03B1) as a primary target of lycopene, crucial for activating the glutathione system because GW6471, a PPARu03B1 antagonist, blocked lycopene-induced GPX4 activation. Furthermore, nuclear factor erythroid 2-related factor 2 (Nrf2) played a crucial role in lycopeneu2019s impact on iron metabolism-related proteins ferritin heavy chain 1 and transferrin receptor 1. Notably, when inhibiting PPARu03B1 or Nrf2 in MCD diet-fed mice by GW6471 or ML385, lycopeneu2019s protective effects against ferroptosis and NASH progression diminished. These findings underscore the crucial role of PPARu03B1-mediated glutathione system activation and Nrf2-mediated iron metabolism modulation in lycopeneu2019s anti-ferroptosis effects.

The global burden of non-alcoholic steatohepatitis (NASH) is on the rise. Researchers recognize inhibiting ferroptosis, a form of cell death leading to iron-dependent oxidative damage, as a promising therapy for treating NASH. Lycopene, a natural antioxidant compound, exhibits various pharmacological properties. However, the anti-NASH efficacy of the dietary recommended concentration of lycopene and the role of lycopene in combating ferroptosis in NASH have remained unclear. Our study investigated lycopene’s impact on ferroptosis in various diet-induced mouse NASH models and corresponding cellular models, unveiling its anti-inflammatory and anti-fibrotic effects. Our findings demonstrated that lycopene notably reduced ferroptosis in methionine- and choline-deficient (MCD) diet-fed mice and a normal mouse hepatocyte cell line (NCTC1469) by restoring balanced ferrous iron levels, lipid reactive oxygen species, and normal mitochondrial morphology. These effects were linked to the regulation of ferroptosis markers glutathione peroxidase 4 (GPX4) and prostaglandin G/H synthase 2. Additionally, lycopene’s anti-ferroptosis action was validated in mice fed a high-fat, high-cholesterol diet and HepG2 cells treated with free fatty acid. Our transcriptomic analysis highlighted peroxisome proliferator-activated receptor α (PPARα) as a primary target of lycopene, crucial for activating the glutathione system because GW6471, a PPARα antagonist, blocked lycopene-induced GPX4 activation. Furthermore, nuclear factor erythroid 2-related factor 2 (Nrf2) played a crucial role in lycopene’s impact on iron metabolism-related proteins ferritin heavy chain 1 and transferrin receptor 1. Notably, when inhibiting PPARα or Nrf2 in MCD diet-fed mice by GW6471 or ML385, lycopene’s protective effects against ferroptosis and NASH progression diminished. These findings underscore the crucial role of PPARα-mediated glutathione system activation and Nrf2-mediated iron metabolism modulation in lycopene’s anti-ferroptosis effects.

Background: Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD) account for the vast majority of neurodegenerative dementias. AD and FTLD have different clinical phenotypes with a genetic overlap between them and other dementias. Objective: This study aimed to identify the genetic spectrum of sporadic AD and FTLD in the Chinese population. Methods: A total of 74 sporadic AD and 29 sporadic FTLD participants were recruited. All participants underwent whole-exome sequencing (WES) and testing for a hexanucleotide expansion in C9orf72 was additionally performed for participants with negative WES results. Results: Four known pathogenic or likely pathogenic variants, including PSEN1 (p.G206D), MAPT (p.R5H), LRRK2 (p.W1434*), and CFAP43 (p.C934*), were identified in AD participants, and 1 novel pathogenic variant of ANXA11 (p.D40G) and two known likely pathogenic variants of MAPT (p.D177V) and TARDBP (p.I383V) were identified in FTLD participants. Twenty-four variants of uncertain significance as well as rare variants in risk genes for dementia, such as ABCA7, SORL1, TRPM7, NOS3, MPO, and DCTN1, were also found. Interestingly, several variants in participants with semantic variant primary progressive aphasia were detected. However, no participants with C9orf72 gene variants were found in the FTLD cohort. Conclusions: There was a high frequency of genetic variants in Chinese participants with sporadic AD and FTLD and a complex genetic overlap between these two types of dementia and other neurodegenerative diseases.

Early prenatal diagnosis of genetic diseases allows for timely intervention or prevention of  the diseases in newborns. Conventional prenatal diagnosis of most genetic diseases relies on testing fetal DNA obtained by invasive procedures such as amniocentesis or chorionic villus sampling, which are associated with small risks of fetal loss. Maternal circulating blood contains cell-free DNA (cfDNA) from the fetal genome and can thus be used to noninvasively detect fetal genetic diseases such as chromosomal abnormalities, copy number variants, and single gene diseases. However, due to the presence of a high level of maternal cfDNA in the maternal blood stream, a relative haplotype dosage (RHDO) analysis is required to detect the mutant loci in the fetal genome when performing noninvasive prenatal diagnosis (NIPD) by massively parallel sequencing (MPS) of cfDNA. In this chapter, we describe a protocol utilizing the RHDO strategy for NIPD of any gene of interest associating with single gene diseases.

Background With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. Methods In this study, we introduced a whole WGS pipeline for genetic disorders, which included the entire process from obtaining a sample to clinical reporting. All samples that underwent WGS were constructed using polymerase chain reaction (PCR)-free library preparation protocols and sequenced on the MGISEQ-2000 platform. Bioinformatics pipelines were developed for the simultaneous detection of various types of variants, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and balanced rearrangements, mitochondrial (MT) variants, and other complex variants such as repeat expansion, pseudogenes and absence of heterozygosity (AOH). A semiautomatic pipeline was developed for the interpretation of potential SNVs and CNVs. Forty-five samples (including 14 positive commercially available samples, 23 laboratory-held positive cell lines and 8 clinical cases) with known variants were used to validate the whole pipeline. Results In this study, a whole WGS pipeline for genetic disorders was developed and optimized. Forty-five samples with known variants (6 with SNVs and Indels, 3 with MT variants, 5 with aneuploidies, 1 with triploidy, 23 with CNVs, 5 with balanced rearrangements, 2 with repeat expansions, 1 with AOHs, and 1 with exon 7–8 deletion of SMN1 gene) validated the effectiveness of our pipeline. Conclusions This study has been piloted in test development, optimization, and validation of the WGS pipeline for genetic disorders. A set of best practices were recommended using our pipeline, along with a dataset of positive samples for benchmarking.

BACKGROUND:Deafness, autosomal recessive 16 (DFNB16) is caused by compound heterozygous or homozygous variants in STRC and is the second most common form of genetic hearing loss. Due to the nearly identical sequences of STRC and the pseudogene STRCP1, analysis of this region is challenging in clinical testing.METHODS:We developed a method that accurately identifies the copy number of STRC and STRCP1 using standard short-read genome sequencing. Then, we used whole genome sequencing (WGS) data to investigate the population distribution of STRC copy number in 6813 neonates and the correlation between STRC and STRCP1 copy number.RESULTS:The comparison of WGS results with multiplex ligation-dependent probe amplification demonstrated high sensitivity (100%; 95% CI, 97.5%-100%) and specificity (98.8%; 95% CI, 97.7%-99.5%) in detecting heterozygous deletion of STRC from short-read genome sequencing data. The population analysis revealed that 5.22% of the general population has STRC copy number changes, almost half of which (2.33%; 95% CI, 1.99%-2.72%) were clinically significant, including heterozygous and homozygous STRC deletions. There was a strong inverse correlation between STRC and STRCP1 copy number.CONCLUSIONS:We developed a novel and reliable method to determine STRC copy number based on standard short-read based WGS data. Incorporating this method into analytic pipelines would improve the clinical utility of WGS in the screening and diagnosis of hearing loss. Finally, we provide population-based evidence of pseudogene-mediated gene conversions between STRC and STRCP1.

Abstract Background Usher syndrome is a condition characterized by partial or total hearing loss and progressive pigmentary retinopathy. Usher syndrome type 1F is caused by biallelic loss‐of‐function variants in Protocadherin 15 (PCDH15), which encodes the PCDH15 protein that plays an important role in the morphogenesis and cohesion of stereocilium bundles and retinal photoreceptor cell maintenance and function. Methods We report a child with bilateral nonsyndromic sensorineural hearing loss who received an inconclusive diagnosis based on clinical gene panel testing, which identified a paternal heterozygous nonsense variant (NM_033056.4: c.733C>T, p.R245*) in PCDH15. This variant has been described as a founder variant in the Ashkenazi Jewish population. Results A novel deep‐intronic variant (NM_033056.4: c.705+3767_705+3768del) inherited from the patient's mother was identified by trio‐based whole‐genome sequencing (WGS). A minigene splicing assay revealed that c.705+3767_705+3768del results in aberrant retention of 50 or 68 bp of intron 7. Conclusion Our genetic test results provided precise genetic counseling and prenatal diagnosis for this family, and our findings highlight the power of WGS for detecting deep‐intronic variants in patients with undiagnosed rare diseases. Additionally, this case expands the variant spectrum of the PCDH15 gene and our results support the extremely low carrier frequency of c.733C>T in the Chinese population.

Background As an adjunct to diagnostic exome sequencing and whole-genome sequencing, RNA sequencing (RNA-seq) has been demonstrated to improve diagnostic yield for Mendelian diseases. However, systematic evaluation of the associated experimental and computational processes and the establishment of robust and efficient practices for RNA diagnostics implemented in the clinic to analyse readily accessible whole blood samples are still required. Methods We simulated clinical conditions in which each patient’s sample is tested only once, and we evaluated the two typical experimental protocols (polyA-selection and rRNA depletion) by comparing the expression profiles, aberrant splicing events and monoallelic expression (MAE) identified from 11 patients in clinical settings with different bioinformatics software. Results We demonstrated that a higher proportion of unique reads from polyA-selection than rRNA depletion were mapped to exons or exon – intron junction regions (84.54% vs. 40.14%), resulting in more detectable OMIM genes (TPM > 1) in the blood (65.29% vs. 59.79%); thus, the rRNA depletion method requires a median of 258 more valid reads per gene to achieve the same level of gene quantification. Moreover, although the transcriptome profiling of protein-coding genes in the two methods is highly correlated, polyA-selection offers more sensitive detection of MAE variants and aberrant splicing under common filtering conditions in combination with DROP. Conclusions A combination of polyA+ and DROP is recommended when implementing blood-based RNA-seq for the diagnosis of Mendelian diseases in clinical practice, and filtering criteria for aberrant expression, aberrant splicing and MAE variants are suggested for reference. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study did not receive any funding ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was approved by the Ethics Committee of Peking Union Medical College Hospital. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

BACKGROUNDGenome-wide noninvasive prenatal testing identifies several rare autosomal trisomies in the general obstetrical population, but its use is questioned by its low positive predictive value. Furthermore, the origin of rare autosomal trisomies and the clinical effect of reporting them has not been sufficiently investigated. In addition, professional societies express their need for data assessing the clinical use of genome-wide noninvasive prenatal testing for rare autosomal trisomies for years.OBJECTIVEThis study aimed to investigate the origin of rare autosomal trisomies and the clinical effect of disclosing rare autosomal trisomies in clinical settings.STUDY DESIGNWomen who received noninvasive prenatal testing between March 2021 and March 2022 were prospectively enrolled. Clinical follow-up and cytogenetic and molecular investigations were performed. Posthoc analysis was performed to investigate the association between placental mosaicism and clinical outcomes.RESULTSOverall, 154 rare autosomal trisomies were identified in 89,242 pregnancies (0.17%) through noninvasive prenatal testing. In the 120 cases in which cytogenetic and molecular investigations were carried out, the rare autosomal trisomies were found to originate from true fetal mosaicism (n=5), uniparental disomy (n=5), maternal mosaic trisomy (n=3), maternal malignancy (n=1), and confined placental mosaicism (n=106). Clinical follow-up showed that 40% of all rare autosomal trisomy cases had adverse perinatal outcomes. In women with false-positive noninvasive prenatal testing results originating from confined placental mosaicism, the frequency of adverse perinatal outcomes was 26%. More importantly, the placental mosaicism ratio revealed by noninvasive prenatal testing was significantly higher in women who experienced adverse perinatal outcomes than those who did not (0.688 vs 0.332; P<.001).CONCLUSIONWomen with noninvasive prenatal testing results indicative of rare autosomal trisomies are at risk of adverse perinatal outcomes, and that risk can be stratified using chromosomes and the mosaicism ratio revealed by noninvasive prenatal testing. Our data are valuable for obstetrical caregivers advising a patient with a noninvasive prenatal testing result indicative of a rare autosomal trisomy and a false-positive diagnosis and for managing risks during pregnancy.

Background: Accurate and consistent interpretation of sequence variants is integral to the delivery of safe and reliable diagnostic genetic services. To standardize the interpretation process, in 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published a joint guideline based on different lines of evidence for the classification of sequence variants in Mendelian diseases. The generality of this guideline necessitates the application of expert judgment when evaluating and weighing evidence for variant interpretation. The Clinical Genome Resource (ClinGen) assembles Variant Curation Expert Panels (VCEPs) to perform gene- and disease-specific modifications of the ACMG/AMP framework. The ClinGen Hemoglobinopathy VCEP was created collaboratively between the ITHANET portal and the Global Globin Network of the Human Variome Project towards comprehensive annotation of all variants related to hemoglobinopathies. Aim: The adaptation of the ACMG/AMP variant interpretation guidelines of use in hemoglobinopathies. Methods: The Hemoglobinopathy VCEP focuses on the review and annotation of variants located in the globin gene clusters, namely α-globin locus (NG_000006), which includes genes HBA1, HBA2 and HBZ, and β-globin locus (NG_000007) which includes genes HBB, HBD, HBG1, HBG2 and HBE and the regulatory element LCRB. Using a consensus approach and guidance by the ClinGen Sequence Variant Interpretation Working Group, the Hemoglobinopathy VCEP has prepared a pre-final version of the specified ACMG/AMP criteria for hemoglobinopathies. Results: The Hemoglobinopathy VCEP developed disease-specific rules for sequence variant classification based on evidence criteria that assess variant frequency, variant types and disease causality, protein domains and mutational hotspots implicated in disease, clinical manifestations, segregation, in silico predictions and functional evidence. Conclusions: For the first time, the Hemoglobinopathy VCEP will provide a standardised classification of the pathogenicity of variants related to hemoglobinopathies. The Hemoglobinopathy VCEP specifications were approved by ClinGen in April 2021 (Step 2 approval), which initiated the process of further validation and adaptation with known globin gene variants in a pilot study (toward Step 3 approval). References 1. Kountouris P et al, Human Mutation 2021, doi: 10.1002/humu.24280

Artemisinin and its derivatives (ARTs) can kill malaria parasites, but their mechanism is not entirely clear. Haem or iron (HI) activates ARTs to produce free radicals that kill malaria parasites, but adding iron supply did not enhance, but attenuated, the antimalarial effect of ARTs, suggesting that their free-radical-effect (FRE) was not their only antimalarial mechanism. Here, using single-cell RNA sequencing analysis of Plasmodium yoelii 17XNL-infected erythrocytes, we proposed that the stages most sensitive to ARTs contained a potential cycle from haem degradation releasing iron to the activation of pentose-phosphate-pathway by iron. Furthermore, artemether could combine with haem to form four adducts and disturb the aggregation of hemozoin. Especially, adding iron supply antagonized the antimalarial effect, suggesting that ARTs could form ARTs-HI complex to disturb the use of HI, thereby killing parasites. Thus, the HI-use-disturbance and FRE constitute the double-kill antimalarial mechanism of ARTs, simultaneously suggesting the mechanisms underlying ARTs resistance.Funding Information: This research was supported by Innovation Program of Shanghai Municipal Education Commission (201901070007E00017).Declaration of Interests: The authors declare no competing interests.Ethics Approval Statement: This study was carried out in 579 strict accordance with the recommendations of the Regulations for the Administration of Affairs Concerning 580 Experimental Animals of the State Science and Technology Commission. The protocol was approved by the 581 Internal Review Board of Tongji University School of Medicine (TJLAC-017–039).

Background: Hearing loss affects approximately two out of every 1,000 newborns. Genetic factors and congenital cytomegalovirus (CMV) infections account for around 90% of the etiology. The purpose of this study was to develop and test a whole genome sequencing (WGS) approach to detect deafness-related genetic variants and CMV infections simultaneously in newborns. Method: Deafness-related genes causing congenital or childhood hearing loss were curated and selected for newborn screening. Nine dried blood spots from newborns with known genetic variants (n = 6) or CMV infections (n = 3) were employed to develop and validate the WGS testing and analytic pipeline. We then pilot tested the WGS analysis on 51 de-identified clinical samples. Results: 92 gene-disease pairs were selected for screening hearing loss in newborns. In the validation test, WGS accurately detected all types of genetic variants, including single nucleotide variations, insertions/deletions, and copy number variations in the nuclear or mitochondrial genome. Sequence reads mapping to the CMV reference genome were discovered in CMV infected samples. In the pilot test, WGS identified nine out of 51 (18%) newborns carrying pathogenic variants associated with deafness. Conclusion: WGS can simultaneously detect genetic variants and CMV infections in dried blood spot specimens from newborns. Our study provides proof of principle that genome sequencing can be a promising alternative for newborn screening of hearing loss.

In this study, we report two novel thalassemia variants detected in Chinese individuals using targeted NGS technology. We detected a novel frameshift variant, HBB: c.181delG, in a 32-year-old Chinese individual. This novel variant [a single nucleotide deletion at nucleotide 181 of codon 60 (-G)], was detected by targeted next generation sequencing (NGS), resulting in a stop codon at codon 60 in exon 2 of the HBB gene. The impact of this novel variant was further analyzed by an in vitro model. We also identified a novel in-frame variant, HBA1: c.121_126delAAGACC [codons 40/41 (-AAGACC)], in another Chinese individual in this study. We named these two novel variants, HBB: c.181delG and HBA1: c.121_126delAAGACC according to the Human Genome Variation Society (HGVS), which were detected by the first author. These two novel variants have expanded the mutation spectrum of thalassemia and it would be beneficial for carrier screening, genetic counseling and prenatal diagnosis (PND) of thalassemia.

Whole genome sequencing (WGS) is a powerful tool for postnatal genetic diagnosis, but relevant clinical studies in the field of prenatal diagnosis are limited. The present study aimed to prospectively evaluate the utility of WGS compared with chromosomal microarray (CMA) and whole exome sequencing (WES) in the prenatal diagnosis of fetal structural anomalies. We performed trio WGS (≈40-fold) in parallel with CMA in 111 fetuses with structural or growth anomalies, and sequentially performed WES when CMA was negative (CMA plus WES). In comparison, WGS not only detected all pathogenic genetic variants in 22 diagnosed cases identified by CMA plus WES, yielding a diagnostic rate of 19.8% (22/110), but also provided additional and clinically significant information, including a case of balanced translocations and a case of intrauterine infection, which might not be detectable by CMA or WES. WGS also required less DNA (100 ng) as input and could provide a rapid turnaround time (TAT, 18 ± 6 days) compared with that (31 ± 8 days) of the CMA plus WES. Our results showed that WGS provided more comprehensive and precise genetic information with a rapid TAT and less DNA required than CMA plus WES, which enables it as an alternative prenatal diagnosis test for fetal structural anomalies.

A novel mutation, HBB: c.393T>G on the HBB gene, was detected in two hypochromic microcytic anemia patients from Yulin, in the Guangxi Province of the People’s Republic of China (PRC), by next-generation sequencing (NGS). It is a nonsense mutation causing a stop codon at amino acid 131 in exon 3 of the HBB gene. It was found in a heterozygous state in two patients who both presented severe anemia during pregnancy and moderate anemia before pregnancy; Hb A2 levels were slightly increased (more than 4.0%) in both patients. It was also detected in the father of one of the patients. This mutation was pathogenic, and caused the dominant thalassemia-like phenotypes in the two patients.

We detected a novel frameshift variant (HBA1: c.263delA) and - -SEA (Southeast Asian), deletion in a 28-year-old Chinese woman with α-thalassemia (α-thal). This novel variant (a single nucleotide deletion at nucleotide 263 of codon 87) was detected by targeted next generation sequencing (NSG), resulting in a stop codon at amino acid 102 in exon 2 of the HBA1 gene. We also identified a novel heterozygous insertion (HBA2: c.376dupC) in a 24-year-old Chinese woman through screening for thalassemia. These two novel variants have expanded the mutation spectrum of α-thal and it would be beneficial for carrier screening, genetic counseling and prenatal diagnosis (PND) of α-thal.

Background Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated. Methods Here, the performance of WGS in NA12878, the YH cell line, and the Chinese trios were measured by assessing their sensitivity, PPV, depth and breadth of coverage using MGISEQ-2000. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using the family-based trio design for the Chinese trios. We further developed a systematic WGS pipeline for the analysis of 8 clinical cases. Results In general, the sensitivity and PPV for SNV/indel detection increased with mean depth and reached a plateau at an ~ 40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was > 99.25% and > 99.50%, respectively, and the PPV was 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV were still not 100% even with a mean depth of ~ 150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size less than 1 kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~ 40X) was better than WES (~ 120X). Among the Chinese trios with an ~ 40X mean depth, the sensitivity among offspring was > 99.48% and > 96.36% for SNP and indel detection, and the PPVs were 99.86% and 97.93%. All 12 previously validated variants in the 8 clinical cases were successfully detected using our WGS pipeline. Conclusions The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. It would be advisable for clinical scientists to determine the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.