Recurrent neural network for predicting absence of heterozygosity from low pass WGS with ultra-low depth.

BACKGROUND: The absence of heterozygosity (AOH) is a kind of genomic change characterized by a long contiguous region of homozygous alleles in a chromosome, which may cause human genetic disorders. However, no method of low-pass whole genome sequencing (LP-WGS) has been reported for the detection of AOH in a low-pass setting of less than onefold. We developed a method, termed CNVseq-AOH, for predicting the absence of heterozygosity using LP-WGS with ultra-low sequencing data, which overcomes the sparse nature of typical LP-WGS data by combing population-based haplotype information, adjustable sliding windows, and recurrent neural network (RNN). We tested the feasibility of CNVseq-AOH for the detection of AOH in 409 cases (11 AOH regions for model training and 863 AOH regions for validation) from the 1000 Genomes Project (1KGP). AOH detection using CNVseq-AOH was also performed on 6 clinical cases with previously ascertained AOHs by whole exome sequencing (WES). RESULTS: Using SNP-based microarray results as reference (AOHs detected by CNVseq-AOH with at least a 50% overlap with the AOHs detected by chromosomal microarray analysis), 409 samples (863 AOH regions) in the 1KGP were used for concordant analysis. For 784 AOHs on autosomes and 79 AOHs on the X chromosome, CNVseq-AOH can predict AOHs with a concordant rate of 96.23% and 59.49% respectively based on the analysis of 0.1-fold LP-WGS data, which is far lower than the current standard in the field. Using 0.1-fold LP-WGS data, CNVseq-AOH revealed 5 additional AOHs (larger than 10 Mb in size) in the 409 samples. We further analyzed AOHs larger than 10 Mb, which is recommended for reporting the possibility of UPD. For the 291 AOH regions larger than 10 Mb, CNVseq-AOH can predict AOHs with a concordant rate of 99.66% with only 0.1-fold LP-WGS data. In the 6 clinical cases, CNVseq-AOH revealed all 15 known AOH regions. CONCLUSIONS: Here we reported a method for analyzing LP-WGS data to accurately identify regions of AOH, which possesses great potential to improve genetic testing of AOH.

Defensins regulate cell cycle: Insights of defensins on cellular proliferation and division.

Defensins are a class of small antimicrobial peptides that play a crucial role against pathogens. However, recent research has highlighted defensins exhibit the ability to influence cell cycle checkpoints, promoting or inhibiting specific phases such as G1 arrest or S/M transition. By regulating the cell cycle, defensins impact the proliferation of normal and cancerous cells, with implications for cancer development and progression. Dysregulation of defensin expression can disrupt the delicate balance of cell cycle regulation, leading to uncontrolled cell growth and an increased risk of tumor formation. Defensins contribute to the resolution of inflammation, stimulate angiogenesis, and enhance the migration and proliferation of cells involved in tissue repair. Furthermore, The ability of defensins to respond to microenvironmental changes further demonstrates the significance of these peptides in host defense mechanisms and immune function. By adjusting their expression, defensins continue to combat pathogens effectively and maintain homeostasis within the body. This review highlights the multifaceted role of defensins in regulating the cell cycle and their broader implications in cancer progression, tissue repair, and microenvironmental response.

Carrier rate of thalassemia among 25,910 high school students in Shaoguan area, China.

OBJECTIVES: As one of the most common hereditary diseases, thalassemia affects a large number of people in China. The aim of this study was to investigate the feasibility of a method based on next-generation sequencing (NGS) for screening of thalassemia carriers among high school students in the Shaoguan area. MATERIALS AND METHODS: The NGS-based method was performed using 25,910 high school students recruited from 38 schools. The screening yield was systematically analyzed. Before screening, a lecture on how the disease is inherited, the symptoms of thalassemia, and how to prevent it was given to 28,780 students. RESULTS: Implying successful delivery of information on the disease, 90.03% (25,910 of 28,780) of the students agreed to join this program for thalassemia screening. A thalassemia carrier rate of 15.99% (4144 of 25,910) was found. Also, 69 rare genotypes (28 of α-thalassemia and 41 of ß-thalassemia) and 9 novel variants were identified. CONCLUSIONS: This NGS-based method provided a feasible platform for high school population thalassemia screening. Combined with a clinical follow-up strategy, it could help eventually to prevent the births of affected children.

Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs.

BACKGROUND: Low-pass genome sequencing (LP GS) has shown distinct advantages over traditional methods for the detection of mosaicism. However, no study has systematically evaluated the accuracy of LP GS in the detection of mosaic aneuploidies and copy number variants (CNVs) in prenatal diagnosis. Moreover, the influence of sequencing depth on mosaicism detection of LP GS has not been fully evaluated. METHODS: To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and mosaic CNVs, 27 samples with known aneuploidies and CNVs and 1 negative female sample were used to generate 6 simulated samples and 21 virtual samples, each sample contained 9 different mosaic levels. Mosaic levels were simulated by pooling reads or DNA from each positive sample and the negative sample according to a series of percentages (ranging from 3 to 40%). Then, the influence of sequencing depth on LP GS in the detection of mosaic aneuploidies and CNVs was evaluated by downsampling. RESULTS: To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and CNVs, a comparative analysis of mosaic levels was performed using 6 simulated samples and 21 virtual samples with 35 M million (M) uniquely aligned high-quality reads (UAHRs). For mosaic levels > 30%, the average difference (detected mosaic levels vs. theoretical mosaic levels) of 6 mosaic CNVs in simulated samples was 4.0%, and the average difference (detected mosaic levels vs. mosaic levels of Y chromosome) of 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples was 2.7%. Furthermore, LP GS had a higher detection rate and accuracy for the detection of mosaic aneuploidies and CNVs of larger sizes, especially mosaic aneuploidies. For depth evaluation, the results of LP GS in downsampling samples were compared with those of LP GS using 35 M UAHRs. The detection sensitivity of LP GS for 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples increased with UAHR. For mosaic levels > 30%, the total detection sensitivity reached a plateau at 30 M UAHRs. With 30 M UAHRs, the total detection sensitivity was 99.2% for virtual samples. CONCLUSIONS: We demonstrated the accuracy of LP GS in mosaicism detection using simulated data and virtual samples, respectively. Thirty M UAHRs (single-end 35 bp) were optimal for LP GS in the detection of mosaic aneuploidies and most mosaic CNVs larger than 1.48 Mb (Megabases) with mosaic levels > 30%. These results could provide a reference for laboratories that perform clinical LP GS in the detection of mosaic aneuploidies and CNVs.

Transnasal negative pressure therapy for accelerating healing and improving the prognosis of pharyngocutaneous fistula.

BACKGROUND: Pharyngocutaneous fistula (PCF) is one of the most common complications of total laryngectomy. This study is to investigate the efficacy of a novel platform called transnasal negative pressure therapy (TNPT) in the management of PCF. METHODS: We retrospectively reviewed 47 patients who underwent total laryngectomy between April 2015 and February 2021 and developed PCF in our hospital. We focused on the healing rate, dressing change frequency, and healing time between the TNPT and non-TNPT groups. The 2 years overall survival (OS) was compared through the log-rank test. RESULTS: There were 18 patients in the TNPT group and 29 in the non-TNPT group. There was no significant between-group difference in the healing rate (chi-square test). However, the frequency of dressing changes was significantly lower (p < 0.001) and the healing time was significantly shorter (p = 0.0194) in the TNPT group than in the non-TNPT group. The 2-year OS rate was significantly higher in the TNPT group (p = 0.0473, log-rank test). CONCLUSION: TNPT promoted wound healing after surgery for PCF and improved the 2-year OS rate. This tool is worthy of clinical application and promotion.

Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform.

Most variations in the human genome refer to single-nucleotide variation (SNV), small fragment insertions and deletions, and genomic copy number variation (CNV). Many human diseases including genetic disorders are associated with variations in the genome. These disorders are often difficult to be diagnosed because of their complex clinical conditions, therefore, an effective detection method is needed to facilitate clinical diagnosis and prevent birth defects. With the development of high-throughput sequencing technology, the method of targeted sequence capture chip has been extensively used owing to its high throughput, high accuracy, fast speed, and low cost. In this study, we designed a chip that potentially captured the coding region of 3043 genes associated with 4013 monogenic diseases, with an addition of 148 chromosomal abnormalities that can be identified by targeting specific regions. To assess the efficiency, a strategy of combining the BGISEQ500 sequencing platform with the designed chip was utilized to screen variants in 63 patients. Eventually, 67 disease-associated variants were found, 31 of which were novel. The results of the evaluation test also show that this combined strategy complies with the requirements of clinical testing and has proper clinical application value.

Validation and depth evaluation of low-pass genome sequencing in prenatal diagnosis using 387 amniotic fluid samples.

BACKGROUND: Low-pass genome sequencing (LP GS) is an alternative to chromosomal microarray analysis (CMA). However, validations of LP GS as a prenatal diagnostic test for amniotic fluid are rare. Moreover, sequencing depth of LP GS in prenatal diagnosis has not been evaluated. OBJECTIVE: The diagnostic performance of LP GS was compared with CMA using 375 amniotic fluid samples. Then, sequencing depth was evaluated by downsampling. RESULTS: CMA and LP GS had the same diagnostic yield (8.3%, 31/375). LP GS showed all copy number variations (CNVs) detected by CMA and six additional variant of uncertain significance CNVs (>100 kb) in samples with negative CMA results; CNV size influenced LP GS detection sensitivity. CNV detection was greatly influenced by sequencing depth when the CNV size was small or the CNV was located in the azoospermia factor c (AZFc) region of the Y chromosome. Large CNVs were less affected by sequencing depth and more stably detected. There were 155 CNVs detected by LP GS with at least a 50% reciprocal overlap with CNVs detected by CMA. With 25 M uniquely aligned high-quality reads (UAHRs), the detection sensitivity for the 155 CNVs was 99.14%. LP GS using samples with 25 M UAHRs showed the same performance as LP GS using total UAHRs. Considering the detection sensitivity, cost and interpretation workload, 25 M UAHRs are optimal for detecting most aneuploidies and microdeletions/microduplications. CONCLUSION: LP GS is a promising, robust alternative to CMA in clinical settings. A total of 25 M UAHRs are sufficient for detecting aneuploidies and most microdeletions/microduplications.

Test development, optimization and validation of a WGS pipeline for genetic disorders.

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.

Source, Distribution and Potential Risk of Antimony in Water and Sediments of Danjiangkou Reservoir: Impact from Dam.

Danjiangkou Reservoir is the water source of the mid-route of the South-to-North Water Transfer Project. The source, distribution and potential risk of antimony in its water and sediments are rarely reported. In this study, symmetrical investigation results demonstrated that the concentration of antimony in the Han sub-reservoir and water in front of the dam fluctuated at about 0.9 mg L-1, while it was relatively higher and increased with the distance from the dam in Dan sub-reservoir water, with an annual average of 0.93~3.15 mg L-1. In recent years, the concentration of antimony in the Danjiangkou Reservoir showed a downward trend, and the difference between the Han and Dan sub-reservoirs decreased significantly. The antimony in the sediments in the reservoir was primarily derived from the inflowing rivers, and it was higher in the Dan sub-reservoir than in the Han sub-reservoir. The concentration of antimony in the water in the reservoir was considerably higher than the background value in the watersheds, indicating that there is an external input with decreasing input intensity. The content of antimony in the sediments in the reservoir and its inflow rivers was substantially higher than the background value of watersheds, indicating that there is a certain degree of enrichment. In addition, the antimony mining industry in the water source area poses a risk to the water safety of the reservoir. Antimony is not a conventional pollutant. Consequently, the collection of antimony monitoring results is a challenging task. Additionally, this study fills the gap in regional antimony research. Furthermore, the ecological risk assessment of antimony in China is still in its infancy. Unquestionably, the study of the temporal and spatial distribution of antimony concentration will be beneficial for the protection of water sources in relevant regions.

Chinese nurses' perceptions on toxic leadership behaviours of nurse managers: A qualitative study.

AIM: The aim of this study is to explore the perceptions of Chinese registered nurses on toxic leadership behaviours of nurse managers and to determine its type, cause and response measures. BACKGROUND: The nurse manager is the front-line leader of the nurses who provide services directly to patients. Previous evidence suggests that toxic leadership behaviours of nurse managers do exist and it is necessary to understand the specifics of it. METHODS: We used phenomenological research methods to conduct semi-structured in-depth interviews among 12 nurses at a tertiary hospital in Wuhan over the period from January to March 2022. And the data were analysed using Colaizzi seven-step analysis method. RESULTS: Four themes were discovered: (a) nurses' perceptions of toxic leadership behaviours; (b) toxic leadership behaviours of nurse managers; (c) reasons for toxic leadership behaviours of nurse managers and (d) measures for toxic leadership behaviours of nurse managers. CONCLUSION: Chinese nurses are exposed to the toxic leadership of nurse managers for multiple reasons and respond differently. IMPLICATIONS FOR NURSING MANAGEMENT: This study helps nursing managers identify which behaviours are harmful to the nurse that require special attention in developing strategies to buffer against nurse managers' toxic leadership.

Performance characterization of PCR-free whole genome sequencing for clinical diagnosis.

ABSTRACT: To evaluate the performance of polymerase chain reaction (PCR)-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection.Five NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing deoxyribonucleic acid (DNA) input and library preparation protocol (PCR-based vs PCR-free protocols for library preparation). The depth of coverage and genotype quality of each sample were compared. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes, and copy number variants. We also developed a systematic WGS pipeline (PCR-free) for the analysis of 11 clinical cases.In general, NA12878-2 (PCR-free WGS) showed better depth of coverage and genotype quality distribution than NA12878-1 (PCR-based WGS). With a mean depth of ∼40×, the sensitivity of homozygous and heterozygous single nucleotide polymorphisms (SNPs) of NA12878-2 showed higher sensitivity (>99.77% and >99.82%) than NA12878-1, and positive predictive value exceeded 99.98% and 99.07%. The sensitivity and positive predictive value of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and copy number variants are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. All the 19 previously confirmed variants in 11 clinical cases were successfully detected by our WGS pipeline (PCR free).Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.

Low expression of lncRNA SBF2-AS1 regulates the miR-302b-3p/TGFBR2 axis, promoting metastasis in laryngeal cancer.

The 5-year survival rate of laryngeal cancer continues to decline, and the laryngeal particularity of the anatomy adversely affects the patient's quality of life. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are closely correlated to key steps in the malignant progression of cancer cells. In this study, we report the role of lncRNA SBF2-AS1/miR-302b-3p/TGFBR2 interactions in the metastasis of laryngeal squamous cell carcinoma (LSCC). We verified that SBF2-AS1 was significantly downregulated in LSCC tissues and cell lines using qRT-PCR analysis. Its low expression was correlated to lymph node metastasis and an advanced clinical stage. More importantly, LSCC patients with low expression of SBF2-AS1 tended to have a poor prognosis. Based on this, we performed gain-of-function and loss-of-function experiments in LSCC cell lines. The results confirmed that knocking down SBF2-AS1 can promote the metastasis of LSCC cells and enhance epithelial-mesenchymal transition phenotype, while the upregulation of SBF2-AS1 expression resulted in the opposite. Our in vivo model verified that SBF2-AS1 overexpression could inhibit LSCC cell metastasis. Subsequent mechanistic studies revealed that SBF2-AS1 acted as a competing endogenous RNA that upregulated the expression of TGFBR2 by endogenous sponging for miR-302b-3p in LSCC cell lines. Moreover, miR-302b-3p overexpression reversed the inhibitory effects on LSCC metastasis induced by upregulation of SBF2-AS1 expression, and inhibition of TGFBR2 expression reversed the effect of SBF2-AS1 on metastasis. Our study proposes SBF2-AS1 as a biomarker to predict the prognosis of LSCC patients and a novel potential therapeutic target.

Deep Learning for Diagnosis and Classification of Obstructive Sleep Apnea: A Nasal Airflow-Based Multi-Resolution Residual Network.

PURPOSE: This study evaluated a novel approach for diagnosis and classification of obstructive sleep apnea (OSA), called Obstructive Sleep Apnea Smart System (OSASS), using residual networks and single-channel nasal pressure airflow signals. METHODS: Data were collected from the sleep center of the First Affiliated Hospital, Sun Yat-sen University, and the Integrative Department of Guangdong Province Traditional Chinese Medical Hospital. We developed a new model called the multi-resolution residual network (Mr-ResNet) based on a residual network to detect nasal pressure airflow signals recorded by polysomnography (PSG) automatically. The performance of the model was assessed by its sensitivity, specificity, accuracy, and F1-score. We built OSASS based on Mr-ResNet to estimate the apnea‒hypopnea index (AHI) and to classify the severity of OSA, and compared the agreement between OSASS output and the registered polysomnographic technologist (RPSGT) score, assessed by two technologists. RESULTS: In the primary test set, the sensitivity, specificity, accuracy, and F1-score of Mr-ResNet were 90.8%, 90.5%, 91.2%, and 90.5%, respectively. In the independent test set, the Spearman correlation for AHI between OSASS and the RPSGT score determined by two technologists was 0.94 (p < 0.001) and 0.96 (p < 0.001), respectively. Cohen's Kappa scores for classification between OSASS and the two technologists' scores were 0.81 and 0.84, respectively. CONCLUSION: Our results indicated that OSASS can automatically diagnose and classify OSA using signals from a single-channel nasal pressure airflow, which is consistent with polysomnographic technologists' findings. Thus, OSASS holds promise for clinical application.

Bacillus thuringiensis cry toxin triggers autophagy activity that may enhance cell death.

Although it is well known that Bacillus thuringiensis Cry toxins kill insect pest by disrupting midgut cells of susceptible larvae through their pore formation activity, it is not clear what intracellular events are triggered after pore formation on the cell membrane of the target cells. Here we analyzed the role of Cry toxins on autophagy activation using several cell lines as models as well as in Helicoverpa armigera larvae. The selected insect cell lines (Hi5, Sl-HP and Sf9) were susceptible to activated Cry1Ca toxin, but only Sl-HP cells were also susceptible to activated Cry1Ac toxin. In contrast, the mammalian cell line 293 T was not susceptible to Cry1Ac or to Cry1Ca. Results show that Cry toxins induced autophagy only in the susceptible cell lines as shown by the analysis of the changes in the ratio of Atg8-PE to Atg8 and by formation of autophagosome dots containing Atg8-PE. The Cry1Ac enhanced autophagy in the midgut tissue of H. armigera larvae. Silencing expression of specific genes by RNAi assays confirmed that the autophagy induced by activated Cry toxins was dependent on AMPK and JNK pathways. Finally, inhibition of autophagy in the cell lines by specific inhibitors or RNAi assays resulted in delayed cell death triggered by Cry toxins, suggesting that the increased autophagy activity observed after toxin intoxication may contribute to cell death.

CNSA: a data repository for archiving omics data.

With the application and development of high-throughput sequencing technology in life and health sciences, massive multi-omics data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly and Variation at present. Moreover, CNSA has created a correlation model of living samples, sample information and analytical data on some projects. Both living samples and analytical data are directly correlated with the sample information. From either one, information or data of the other two can be obtained, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for storing, managing and sharing of omics data. We will continue to improve the data standards and provide free access to open-data resources for worldwide scientific communities to support academic research and the bio-industry. Database URL: https://db.cngb.org/cnsa/.

Down-regulation of lysosomal protein ABCB6 increases gossypol susceptibility in Helicoverpa armigera.

Cotton bollworm (Helicoverpa armigera) is the major insect herbivore of cotton plants. As its larvae feed and grow on cotton, H. armigera can likely tolerate gossypol, the main defense metabolite produced by cotton plants, through detoxification and sequestration mechanisms. Recent reports have shown that various P450 monooxygenases and UDP-glycosyltransferases in H. armigera are involved in gossypol detoxification, while the roles of ABC transporters, another gene family widely associated with metabolite detoxification, remain to be elucidated. Here, we show that ingestion of gossypol-infused artificial diet and cotton leaves significantly induced the expression of HaABCB6 in H. armigera larvae. Knockdown and knockout of HaABCB6 increased sensitivity of H. armigera larvae to gossypol. Moreover, HaABCB6-GFP fusion protein was localized on lysosomes in Hi5 cells and its overexpression significantly enhanced gossypol tolerance in vitro. These experimental results strongly support that HaABCB6 plays an important role in gossypol detoxification by H. armigera.

Design of a liver cancer-specific selector for the analysis of circulating tumor DNA.

Circulating tumor DNA (ctDNA) has been frequently investigated to monitor tumor dynamics and measure tumor burden. This non-invasive method concerning ctDNA has been recognized as a promising biomarker. Recently, next generation sequencing has been used in ctDNA detection by researchers. However, those reports have been limited by modest sensitivity, and only a minority of patients with cancer were applicable. Additionally, a limited number of cases of liver cancer have been analyzed. A more precise method is required to be established to evaluate ctDNA noninvasively. In the present study, a novel method to design a liver cancer-associated chip region (spanning 211 kb, containing 159 genes) was performed with high specificity using International Cancer Genome Consortium datasets. Following evaluation with datasets from The Cancer Genome Atlas and data from 3 patients with liver cancer, the selected regions were demonstrated to be beneficial to locate specific somatic mutations associated with liver cancer therapy and to monitor cancer dynamics in the plasma samples of the patients. In addition to establishing performance benchmarks supporting direct clinical use, the chip designed and the high-resolution sequencing analyses pipeline would allow the development a set of patient specific markers that could monitor the process of cancer with high accuracy and low cost. Furthermore, the present study is essential to understanding the dynamics and providing insight into the basic mechanisms of liver cancer.

Pink Bollworm Resistance to Bt Toxin Cry1Ac Associated with an Insertion in Cadherin Exon 20.

Insecticidal proteins from Bacillus thuringiensis (Bt) are widely used to control insect pests, but their efficacy is reduced when pests evolve resistance. We report on a novel allele (r16) of the cadherin gene (PgCad1) in pink bollworm (Pectinophora gossypiella) associated with resistance to Bt toxin Cry1Ac, which is produced by transgenic cotton. The r16 allele isolated from a field population in China has 1545 base pairs of a degenerate transposon inserted in exon 20 of PgCad1, which generates a mis-spliced transcript containing a premature stop codon. A strain homozygous for r16 had 300-fold resistance to Cry1Ac, 2.6-fold cross-resistance to Cry2Ab, and completed its life cycle on transgenic Bt cotton producing Cry1Ac. Inheritance of Cry1Ac resistance was recessive and tightly linked with r16. Compared with transfected insect cells expressing wild-type PgCad1, cells expressing r16 were less susceptible to Cry1Ac. Recombinant cadherin protein was transported to the cell membrane in cells transfected with the wild-type PgCad1 allele, but not in cells transfected with r16. Cadherin occurred on brush border membrane vesicles (BBMVs) in the midgut of susceptible larvae, but not resistant larvae. These results imply that the r16 allele mediates Cry1Ac resistance in pink bollworm by interfering with the localization of cadherin.

Application of an improved targeted next generation sequencing method to diagnose non­syndromic mental retardation in one step: A case report.

The genetic basis of congenital mental retardation includes chromosomal anomalies and single gene mutations. In addition to chromosome microarray analysis, next­generation sequencing (NGS) and Sanger sequencing have additionally been applied to identify single gene mutations. However, no methods exist to identify the cause of an anomaly in one step. The present study applied an improved targeted NGS method to diagnose an 8­year­old Chinese Han female with mental retardation in one step. The microdeletion 17p11.2 was successfully detected by the improved targeted NGS and no single gene mutations were identified. The same microdeletion was verified using low coverage whole­genome sequencing. Fertility guidance was also given to the patient's parents. In the present study, an improved targeted NGS method was applied to diagnose non­syndromic mental retardation of unknown cause in one step. This improved method has the potential to be developed into a screening panel for the effective diagnosis of genetic abnormalities in non­syndromic mental retardation and other congenital anomalies.

Identification of a Disease-Causing Mutation in a Chinese Patient with Retinitis Pigmentosa by Targeted Next-Generation Sequencing.

PURPOSE: To identify disease-causing mutations in a Chinese patient with retinitis pigmentosa (RP). METHODS: A detailed clinical examination was performed on the proband. Targeted next-generation sequencing (NGS) combined with bioinformatics analysis was performed on the proband to detect candidate disease-causing mutations. Sanger sequencing was performed on all subjects to confirm the candidate mutations and assess cosegregation within the family. RESULTS: Clinical examinations of the proband showed typical characteristics of RP. Three candidate heterozygous mutations in 3 genes associated with RP were detected in the proband by targeted NGS. The 3 mutations were confirmed by Sanger sequencing and the deletion (c.357_358delAA) in PRPF31 was shown to cosegregate with RP phenotype in 7 affected family members, but not in 3 unaffected family members. CONCLUSIONS: The deletion (c.357_358delAA) in PRPF31 was the disease-causing mutation for the proband and his affected family members with RP. To our knowledge, this is the second report of the deletion and the first report of the other 2 mutations in the Chinese population. Targeted NGS combined with bioinformatics analysis proved to be an effective molecular diagnostic tool for RP.