Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor.

Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.

Structural and functional abnormalities and cognitive profiles in older adults with early-onset and late-onset focal epilepsy.

This study aimed to determine the patterns of changes in structure, function, and cognitive ability in early-onset and late-onset older adults with focal epilepsy (OFE). This study first utilized the deformation-based morphometry analysis to identify structural abnormalities, which were used as the seed region to investigate the functional connectivity with the whole brain. Next, a correlation analysis was performed between the altered imaging findings and neuropsychiatry assessments. Finally, the potential role of structural-functional abnormalities in the diagnosis of epilepsy was further explored by using mediation analysis. Compared with healthy controls (n = 28), the area of reduced structural volume was concentrated in the bilateral cerebellum, right thalamus, and right middle cingulate cortex, with frontal, temporal, and occipital lobes also affected in early-onset focal epilepsy (n = 26), while late-onset patients (n = 31) displayed cerebellar, thalamic, and cingulate atrophy. Furthermore, correlation analyses suggest an association between structural abnormalities and cognitive assessments. Dysfunctional connectivity in the cerebellum, cingulate cortex, and frontal gyrus partially mediates the relationship between structural abnormalities and the diagnosis of early-onset focal epilepsy. This study identified structural and functional abnormalities in early-onset and late-onset focal epilepsy and explored characters in cognitive performance. Structural-functional coupling may play a potential role in the diagnosis of epilepsy.

Preoperative Assessment of Blood Vessels and Intratumoral Microbleeds in Brain Tumors Based on a 3D Contrast-Enhanced T1 -Weighted Flow-Sensitive Black-Blood Sequence.

BACKGROUND: Three-dimensional (3D) contrast-enhanced T1 -weighted flow-sensitive black-blood (CE-T1 WI FSBB) is a newly developed black blood sequence by adding motion probing gradient pulses to gradient echo (GRE) sequences, which has important value for the preoperative assessment of tumor brain blood supply vessels and intratumoral microbleeds. PURPOSE: To compare 3D CE-T1 WI FSBB and 3D contrast-enhanced fast spin echo (FSE) sequence for T1 WI for preoperative assessment of blood vessels and microbleeds in brain tumors and to investigate the correlation between visible vessels and microbleeds. STUDY TYPE: Prospective. SUBJECTS: One hundred and seventy-five patients with brain tumors, 65 were male, 110 were female. Including histologically confirmed 73 meningiomas, 23 schwannomas, 20 gliomas, 7 hemangioblastomas, 5 metastases, 2 lymphomas, 2 hemangiopericytomas, 2 germ cell tumors, 1 craniopharyngioma, and 1 cholesteatoma. FIELD STRENGTH/SEQUENCE: A 3-T, CE-T1 WI FSBB, GRE; 3-T, CE-T1 WI, FSE. ASSESSMENT: Three neuroradiologists counted the number of intratumoral vessels on CE-T1 WI and CE-T1 WI FSBB images separately, and they counted the number of intratumoral microbleeds on CE-T1 WI FSBB images. Brain tumors were classified into grade I, grade II, and grade IV according to the World Health Organization (WHO) grading. Differences in the ability of CE-T1 WI FSBB and CE-T1 WI to display intratumoral vessels were compared. The mean counts of three observers were used to study the correlation between vessels and microbleeds. STATISTICAL TESTS: Two-way random intraclass correlation coeficient (ICC) was used for inter-reader agreement regarding intratumoral vessel and microbleed counts, and the linear regression analysis (with F-test) was used to study the correlation between intratumoral vessels and microbleeds based on CE-T1 WI FSBB (α = 0.05). RESULTS: Inter-reader agreements for intratumoral vessel count on CE-T1 WI (ICC = 0.93) and CE-T1 WI FSBB (ICC = 0.92), and the agreement for intratumoral microbleed count on CE-T1 WI FSBB (ICC = 0.99) were excellent. There were statistically significant differences in intratumoral vessel counts between CE-T1 WI and CE-T1 WI FSBB using Mann-Whitney U -test: image readers could identify more intratumoral vessels on CE-T1 WI FSBB images, particularly for meningiomas, schwannomas, gliomas, and WHO grade I tumors. The number of intratumoral vessels had a significant positive effect on the number of intratumoral microbleeds (microbleeds = 5.024 + 1.665 × vessels; F = 11.51). DATA CONCLUSION: More intratumoral vessels could potentially be identified using a 3D CE-T1 WI FSBB sequence compared to a CE-T1 WI sequence, and the number of intratumoral vessels showed a positive linear relationship with the number of intratumoral microbleeds, which might suggest that brain tumors with rich blood supply were more prone to intratumoral microbleeds. EVIDENCE LEVEL: 2 TECHNICAL EFFICACY: Stage 3.

Comprehensive preimplantation genetic testing by massively parallel sequencing.

STUDY QUESTION: Can whole genome sequencing (WGS) offer a relatively cost-effective approach for embryonic genome-wide haplotyping and preimplantation genetic testing (PGT) for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR)? SUMMARY ANSWER: Reliable genome-wide haplotyping, PGT-M, PGT-A and PGT-SR could be performed by WGS with 10× depth of parental and 4× depth of embryonic sequencing data. WHAT IS KNOWN ALREADY: Reduced representation genome sequencing with a genome-wide next-generation sequencing haplarithmisis-based solution has been verified as a generic approach for automated haplotyping and comprehensive PGT. Several low-depth massively parallel sequencing (MPS)-based methods for haplotyping and comprehensive PGT have been developed. However, an additional family member, such as a sibling, or a proband, is required for PGT-M haplotyping using low-depth MPS methods. STUDY DESIGN, SIZE, DURATION: In this study, 10 families that had undergone traditional IVF-PGT and 53 embryos, including 13 embryos from two PGT-SR families and 40 embryos from eight PGT-M families, were included to evaluate a WGS-based method. There were 24 blastomeres and 29 blastocysts in total. All embryos were used for PGT-A. Karyomapping validated the WGS results. Clinical outcomes of the 10 families were evaluated. PARTICIPANTS/MATERIALS, SETTING, METHODS: A blastomere or a few trophectoderm cells from the blastocyst were biopsied, and multiple displacement amplification (MDA) was performed. MDA DNA and bulk DNA of family members were used for library construction. Libraries were sequenced, and data analysis, including haplotype inheritance deduction for PGT-M and PGT-SR and read-count analysis for PGT-A, was performed using an in-house pipeline. Haplotyping with a proband and parent-only haplotyping without additional family members were performed to assess the WGS methodology. Concordance analysis between the WGS results and traditional PGT methods was performed. MAIN RESULTS AND THE ROLE OF CHANCE: For the 40 PGT-M and 53 PGT-A embryos, 100% concordance between the WGS and single-nucleotide polymorphism (SNP)-array results was observed, regardless of whether additional family members or a proband was included for PGT-M haplotyping. For the 13 embryos from the two PGT-SR families, the embryonic balanced translocation was detected and 100% concordance between WGS and MicroSeq with PCR-seq was demonstrated. LIMITATIONS, REASONS FOR CAUTION: The number of samples in this study was limited. In some cases, the reference embryo for PGT-M or PGT-SR parent-only haplotyping was not available owing to failed direct genotyping. WIDER IMPLICATIONS OF THE FINDINGS: WGS-based PGT-A, PGT-M and PGT-SR offered a comprehensive PGT approach for haplotyping without the requirement for additional family members. It provided an improved complementary method to PGT methodologies, such as low-depth MPS- and SNP array-based methods. STUDY FUNDING/COMPETING INTEREST(S): This research was supported by the research grant from the National Key R&D Program of China (2018YFC0910201 and 2018YFC1004900), the Guangdong province science and technology project of China (2019B020226001), the Shenzhen Birth Defect Screening Project Lab (JZF No. [2016] 750) and the Shenzhen Municipal Government of China (JCYJ20170412152854656). This work was also supported by the National Natural Science Foundation of China (81771638, 81901495 and 81971344), the National Key R&D Program of China (2018YFC1004901 and 2016YFC0905103), the Shanghai Sailing Program (18YF1424800), the Shanghai Municipal Commission of Science and Technology Program (15411964000) and the Shanghai 'Rising Stars of Medical Talent' Youth Development Program Clinical Laboratory Practitioners Program (201972). The authors declare no competing interests. TRIAL REGISTRATION NUMBER: N/A.

A whole-genome sequencing-based novel preimplantation genetic testing method for de novo mutations combined with chromosomal balanced translocations.

PURPOSE: To explore a new preimplantation genetic testing (PGT) method for de novo mutations (DNMs) combined with chromosomal balanced translocations by whole-genome sequencing (WGS) using the MGISEQ-2000 sequencer. METHODS: Two families, one with maternal Olmsted syndrome caused by DNM (c.1246C>T) in TRPV3 and a paternal Robertsonian translocation and one with paternal Marfan syndrome caused by DNM (c.4952_4955delAATG) in FBN1 and a maternal reciprocal translocation, underwent PGT for monogenetic disease (PGT-M), chromosomal aneuploidy, and structural rearrangement. WGS of embryos and family members were performed. Bioinformatics analysis based on gradient sequencing depth was performed, and parent-embryo haplotyping was conducted for DNM diagnosis. Sanger sequencing, karyotyping, and chromosomal microarray analysis were performed using an amniotic fluid sample to confirm the PGT results. RESULTS: After 1 PGT cycle, WGS of 2 embryos from the Olmsted syndrome family revealed euploid embryos without DNMs; after 2 cycles, the 11 embryos from the Marfan syndrome family showed only 1 normal embryo without DNM, copy number variations (CNVs), or aneuploidy. Moreover, 1 blastocyst from the Marfan syndrome family was transferred back to the uterus; the amniocentesis test results were confirmed by PGT and a healthy infant was born. CONCLUSIONS: WGS based on parent-embryo haplotypes was an effective strategy for PGT of DNMs combined with a chromosomal balanced translocation. Our results indicate this is a reliable and effective diagnostic method that is useful for clinical application in PGT of patients with DNMs.

Noninvasive prenatal testing (NIPT) in twin pregnancies with treatment of assisted reproductive techniques (ART) in a single center.

OBJECTIVE: The objective of the study is to report the performance of noninvasive prenatal testing (NIPT) in twin pregnancies after the treatment of assisted reproductive technology (ART). METHOD: In two years period, 565 pregnant women with ART twin pregnancies were prospectively tested by NIPT for screening for trisomy 21 (T21), 18 (T18), and 13 (T13) by sequencing cell-free DNA in maternal plasma. Positive NIPT results were confirmed by karyotyping, while negative results were interviewed after delivery. Pregnant decision based on NIPT and confirmation results was discussed during post-test counseling. RESULTS: In total of 565 cases, NIPT had a failure rate of 0.9% (5/565). Four cases of T21 were identified by NIPT and confirmed by karyotyping, resulting in 100% (95%CI 39.8%-100%) positive predictive value. Among 556 cases with NIPT negative results, 506 cases (91.0%) were confirmed by follow-up of postnatal phenotypes, while 33 cases (5.9%) had adverse pregnant outcomes with unconfirmed reasons because of the lack of cytogenetic samples. The remaining 17 cases (3.1%) refused follow-up. No false negative result was reported. CONCLUSION: With apparently high positive predictive value and low false positive rate, NIPT has the potential to be used as a good alternative approach of conventional prenatal screening at the first trimester in ART twin pregnancy. © 2016 John Wiley & Sons, Ltd.

Embryo genome profiling by single-cell sequencing for preimplantation genetic diagnosis in a ß-thalassemia family.

BACKGROUND: The embryonic genome, including genotypes and haplotypes, contains all the information for preimplantation genetic diagnosis, representing great potential for mendelian disorder carriers to conceive healthy babies. METHODS: We developed a strategy to obtain the full embryonic genome for a ß-thalassemia-carrier couple to have a healthy second baby. We carried out sequencing for single blastomere cells and the family trio and further developed the analysis pipeline, including recovery of the missing alleles, removal of the majority of errors, and phasing of the embryonic genome. RESULTS: The final accuracy for homozygous and heterozygous single-nucleotide polymorphisms reached 99.62% and 98.39%, respectively. The aneuploidies of embryos were detected as well. Based on the comprehensive embryonic genome, we effectively performed whole-genome mendelian disorder diagnosis and human leukocyte antigen matching tests. CONCLUSIONS: This retrospective study in a ß-thalassemia family demonstrates a method for embryo genome recovery through single-cell sequencing, which permits detection of genetic variations in preimplantation genetic diagnosis. It shows the potential of single-cell sequencing technology in preimplantation genetic diagnosis clinical practices.

Influence of polypropylene fibers on the tensile mechanical properties of calcium silicate hydrate: molecular simulation.

CONTEXT: This research assesses the influence of polypropylene (PP) fibers, both homopolymer and hydroxylated (PPOH), on the tensile properties of calcium silicate hydrate (C-S-H) composites through molecular dynamics (MD) simulations. Our models explore C-S-H matrices integrated with PP and PPOH fibers at varying polymerization degrees. The results demonstrate that both PP and PPOH fibers significantly influence the tensile strength and Young's modulus of the composites. Notably, PPOH fibers contribute to more substantial mechanical enhancements than PP, attributed to the increased polarity and enhanced intermolecular interactions from the hydroxyl groups. The study reveals a nonlinear relationship between polymer additive content and mechanical performance, with optimal properties at a polymerization degree of 20. Additionally, stress-strain analysis indicates that PPOH composites exhibit superior ductility and fracture energy, particularly at polymerization degrees of 20, showing enhanced ultimate strain and fracture energy by up to 9.6% and 13.9%, respectively, compared to PP counterparts. These results highlight the crucial role of tailored polymer additive composition and chemical modifications in maximizing the mechanical efficacy of C-S-H-based materials, enhancing their durability and structural performance. METHODS: All MD simulations were conducted using LAMMPS. The models employed a combination of Clayff and Cvff force fields. During the entire tensile simulation, the system was configured under the NPT ensemble at 300 K.

Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts.

Preimplantation genetic diagnosis and screening are widely accepted for chromosomal abnormality identification to avoid transferring embryos with genetic defects. Massively parallel sequencing (MPS) is a rapidly developing approach for genome analysis with increasing application in clinical practice. The purpose of this study was to use MPS for identification of aneuploidies and unbalanced chromosomal rearrangements after blastocyst biopsy. Trophectoderm (TE) samples of 38 blastocysts from 16 in vitro fertilization cycles were subjected to analysis. Low-coverage whole genome sequencing was performed using the Illumina HiSeq2000 platform with a novel algorithm purposely created for chromosomal analysis. The efficiency of this MPS approach was estimated by comparing results obtained by an Affymetrix single-nucleotide polymorphism (SNP) array. Whole genome amplification (WGA) products of TE cells were detected by MPS, with an average of 0.07× depth and 5.5% coverage of the human genome. Twenty-six embryos (68.4%) were detected as euploid, while six embryos (15.8%) contained uniform aneuploidies. Four of these (10.5%) were with solely unbalanced chromosomal rearrangements, whereas the remaining two embryos (5.3%) showed both aneuploidies and unbalanced rearrangements. Almost all these results were confirmed by the SNP array, with the exception of one sample, where different sizes of unbalanced rearrangements were detected, possibly due to chromosomal GC bias in array analysis. Our study demonstrated MPS could be applied to accurately detect embryonic chromosomal abnormality with a flexible and cost-effective strategy and higher potential accuracy.

Association of deep medullary veins with the neuroimaging burden of cerebral small vessel disease.

Background: This study aimed to explore the association between deep medullary veins (DMVs) and the neuroimaging burden of cerebral small vessel disease (CSVD). Methods: In this cross-sectional study based on a retrospective analysis, a total of 248 patients (183 males and 65 females; mean age ± standard deviation, 69.5±14.8 years) diagnosed with CSVD with complete imaging and clinical data were enrolled. Neuroimaging markers of CSVD, including white matter hyperintensities, lacunes, prominent perivascular spaces (PVSs), and cerebral microbleeds (CMBs), were identified, and the total burden of CSVD was scored. Both DMV number and DMV score were used for assessment using susceptibility-weighted imaging (SWI). Results: With the exception of perivascular spaces, more severe neuroimaging markers were observed in patients with a higher DMV score. After adjustments were made for age and body mass index (BMI), a higher DMV score (ß=1.39; P<0.001) and smaller DMV number (ß=-2.55; P=0.001) were associated with an increased CSVD burden. The degree of CMBs was independently correlated with both DMV score (ß=1.60; P<0.001) and DMV number (ß=-2.27; P=0.009). The association between lacunes and DMV score was also significant (ß=0.97; P=0.026). Conclusions: Both DMV score and DMV number are potential imaging indicators of CSVD.

Functionalized PEG-PLA nanoparticles for brain targeted delivery of ketoconazole contribute to pregnane X receptor overexpressing in drug-resistant epilepsy.

OBJECTIVE: To develop a functionalized PEG-PLA nanoparticle system containing ketoconazole (KCZ) to overcome the overactivity of pregnane X receptor (PXR) for the treatment of drug-resistant epilepsy (DRE). SIGNIFICANCE: KCZ was developed as a therapy strategy for DRE limited by its lethal hepatotoxicity and minute brain concentration. KCZ-incorporated nanoparticles modified with angiopep-2 (NPs/KCZ) could reduce adverse effects of KCZ and achieve epileptic foci-targeted drug delivery. METHODS: NPs/KCZ was prepared by thin-film hydration method and characterized in vitro and in vivo. The efficacy evaluation of NPs/KCZ was evaluated in a kainic acid (KA)-induced mice model of epilepsy with carbamazepine (CBZ) treatment. RESULTS: The mean particle size and Zeta potential of NPs/KCZ were 17.84 ± 0.33 nm and - 2.28 ± 0.12 mV, respectively. The drug-loading (DL%) of KCZ in nanoparticles was 8.96 ± 0.12 % and the entrapment efficiency (EE%) was 98.56 ± 0.02 %. The critical value of critical micelle concentration was 10-3.3 mg/ml. No obvious cytotoxicity was found in vitro. The behavioral and electrographic seizure activities were obviously attenuated in NPs/KCZ+CBZ group. The CBZ concentration of brain tissues in mice treated with NPs/KCZ+CBZ was significantly increased than those treated with CBZ alone (P = 0.0028). A significantly decreased expression level of PXR and its downstream proteins was observed in NPs/KCZ+CBZ group compared with that in the control and CBZ group (All P < 0.05). CONCLUSION: Our results showed that NPs/KCZ achieved the epileptic foci-targeted delivery of KCZ and ameliorated the efficacy of CBZ on DRE by attenuating the overactivity of PXR.

Supratentorial hemangioblastoma at the anterior skull base: A case report.

BACKGROUND: Hemangioblastoma (HB) is a rare tumor, comprising about 2% of all intracranial tumors. Although it is a benign tumor, due to the abundant blood supply and its close relationship with adjacent cerebral blood vessels, surgical resection is difficult and may cause complications such as bleeding. If HB can be correctly diagnosed before surgery, complications can be avoided by methods such as vascular embolism before surgery. CASE SUMMARY: A 51-year-old male patient was admitted to our hospital because of blurred vision in his left eye for 2 years. Ophthalmological examination revealed oculus dexter vision acuity of 1.0 and oculus sinister vision acuity of 0.6. His left vision had tubular visual field, while his right vision had a partial defect. Computed tomography and magnetic resonance imaging showed a mass lesion at the left anterior base of the skull, which could have been a meningioma. During the operation, the tumor was found to be located at the entrance of the left optic nerve tube, closely adhering to the left optic nerve and the blood supply was extremely abundant. The tumor was carefully separated and diagnosed as HB postoperatively after pathological examination. CONCLUSION: A rare HB at the anterior skull base could be distinguished by its imaging features, which is essential to the surgical procedures.

Peliminary exploration on the differential diagnosis between meningioma and schwannoma using contrast-enhanced T1WI flow-sensitive black-blood sequence.

Introduction: Contrast-enhanced T1WI flow-sensitive black-blood (CE-T1WI FSBB) is a newly developed sequence which had not been widely used for differential diagnosis of brain tumors. Methods: To quantify the pre-operative imaging features of intratumoral microbleeds and intratumoral vessels using CE-T1WI FSBB scan and study the differences in biological behavior of meningiomas and schwannomas underlying the imaging features. Seventy-three cases of meningiomas and 24 cases of schwannomas confirmed by postoperative pathology were included. Two neuroradiologists independently counted intratumoral vessels and intratumoral microbleeds based on CE-T1WI FSBB images. The vessel density index (VDI) and microbleed density index (MDI) were the number of intratumoral vessels and the number of intratumoral microbleeds divided by the tumor volume, respectively. The consistency test of intratumoral vessel count and intratumoral microbleed count based on CE-T1WI FSBB were summarized using 2-way random intraclass correlation coefficients (ICC). Mann-Whitney U-test and chi-square test were used to determine significant differences between meningiomas and schwannomas, and fibrous meningiomas and epithelial meningiomas. P<0.05 was considered statistically significant. Results: The ICC of intratumoral vessels count and intratumoral microbleeds count were 0.89 and 0.99, respectively. There were significant differences in the number of intratumoral microbleeds (P<0.01) and MDI values (P<0.01) between meningiomas and schwannomas. There were no differences in the number of intratumoral vessels (P=0.64), VDI (P=0.17), or tumor volume (P=0.33). There were also differences in the number of intratumoral microbleeds (P<0.01), the MDI value (P<0.01), and the sex of patients (P<0.05) between fibrous meningiomas and epithelial meningiomas. Discussion: CE-T1WI FSBB can be a new technique for differentiating schwannomas from meningiomas, and even different types of meningiomas. Schwannomas have a higher incidence of intratumoral hemorrhage, more intratumoral microbleeds, and higher MDI values than meningiomas, which provides a new basis for preoperative differential diagnosis and treatment decisions.

Sequencing bias: comparison of different protocols of microRNA library construction.

BACKGROUND: MicroRNAs(miRNAs) are 18-25 nt small RNAs playing critical roles in many biological processes. The majority of known miRNAs were discovered by conventional cloning and a Sanger sequencing approach. The next-generation sequencing (NGS) technologies enable in-depth characterization of the global repertoire of miRNAs, and different protocols for miRNA library construction have been developed. However, the possible bias between the relative expression levels and sequences introduced by different protocols of library preparation have rarely been explored. RESULTS: We assessed three different miRNA library preparation protocols, SOLiD, Illumina versions 1 and 1.5, using cloning or SBS sequencing of total RNA samples extracted from skeletal muscles from Hu sheep and Dorper sheep, and then validated 9 miRNAs by qRT-PCR. Our results show that SBS sequencing data highly correlate with Illumina cloning data. The SOLiD data, when compared to Illumina's, indicate more dispersed distribution of length, higher frequency variation for nucleotides near the 3'- and 5'-ends, higher frequency occurrence for reads containing end secondary structure (ESS), and higher frequency for reads that do not map to known miRNAs. qRT-PCR results showed the best correlation with SOLiD cloning data. Fold difference of Hu sheep and Dorper sheep between qRT-PCR result and SBS sequencing data correlated well (r = 0.937), and fold difference of miR-1 and miR-206 among SOLiD cloning data, qRT-PCR and SBS sequencing data was similar. CONCLUSIONS: The sequencing depth can influence the quantitative measurement of miRNA abundance, but the discrepancy caused by it was not statistically significant as high correlation was observed between Illumina cloning and SBS sequencing data. Bias of length distribution, sequence variation, and ESS was observed between data obtained with the different protocols. SOLiD cloning data differ from Illumina cloning data mainly because of distinct methods of adapter ligation. The good correlation between qRT-PCR result and SOLiD data might be due to the similarities of the hybridization-based methods. The fold difference analysis indicated that methods based on hybridization may be superior for quantitative measurement of miRNA abundance. Because of the genome sequence of the sheep is not available, our data may not explain how the entire miRNA bias in the natural miRNAs in sheep or other mammal miRNA expression, unbiased artificially synthesized miRNA will help on evaluating the methodology of miRNA library preparation.

Real-time RT-PCR for H5N1 avian influenza A virus detection.

The recent recurrence of highly pathogenic avian influenza virus A H5N1 was firstly reported in mid-December 2003 and continued through 2005. This study describes a sensitive and specific real-time RT-PCR method for the detection of influenza A subtype H5 and for monitoring virus loads. Using serial dilutions of influenza A H5N1 cultures, this assay reproducibly determined the lowest detection limit to be approximately 5 x 10(-2) 50 % egg infective doses (EID(50)). In contrast, the minimum detection limit was approximately 3 EID(50) in conventional RT-PCR with WHO primers and 10 EID(50) in antigen-capture ELISA. In tests of serial dilutions of in vitro-transcribed influenza A H5 gene RNA, there was linear amplification from 40 copies to 4 x 10(8) copies of target RNA per reaction and approximately six copies, and sometimes even as few as three copies, of target RNA tested positive in our assay. Thirty-five throat swabs from ill birds were tested: 33 samples tested positive using this assay. In comparison, 27, 13 and 19 samples tested positive using conventional RT-PCR, antigen-capture ELISA and virus isolation, respectively. To evaluate further the sensitivity of this real-time RT-PCR, a standard panel and 60 H5N1 isolates that contained different clades of influenza virus A/H5N1 were tested and all tested positive. To evaluate the specificity of the assay, 60 throat swabs from patients infected with influenza virus A H1 were tested; all were negative. Thirteen other viruses were also tested and all tested negative.

Performance Evaluation of NIPT in Detection of Chromosomal Copy Number Variants Using Low-Coverage Whole-Genome Sequencing of Plasma DNA.

OBJECTIVES: The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method. METHOD: A total of 919 archived maternal plasma samples with karyotyping/microarray results, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated. RESULTS: 33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively. CONCLUSION: Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.

Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing.

BACKGROUND: Next generation sequencing (NGS) is now being used for detecting chromosomal abnormalities in blastocyst trophectoderm (TE) cells from in vitro fertilized embryos. However, few data are available regarding the clinical outcome, which provides vital reference for further application of the methodology. Here, we present a clinical evaluation of NGS-based preimplantation genetic diagnosis/screening (PGD/PGS) compared with single nucleotide polymorphism (SNP) array-based PGD/PGS as a control. RESULTS: A total of 395 couples participated. They were carriers of either translocation or inversion mutations, or were patients with recurrent miscarriage and/or advanced maternal age. A total of 1,512 blastocysts were biopsied on D5 after fertilization, with 1,058 blastocysts set aside for SNP array testing and 454 blastocysts for NGS testing. In the NGS cycles group, the implantation, clinical pregnancy and miscarriage rates were 52.6% (60/114), 61.3% (49/80) and 14.3% (7/49), respectively. In the SNP array cycles group, the implantation, clinical pregnancy and miscarriage rates were 47.6% (139/292), 56.7% (115/203) and 14.8% (17/115), respectively. The outcome measures of both the NGS and SNP array cycles were the same with insignificant differences. There were 150 blastocysts that underwent both NGS and SNP array analysis, of which seven blastocysts were found with inconsistent signals. All other signals obtained from NGS analysis were confirmed to be accurate by validation with qPCR. The relative copy number of mitochondrial DNA (mtDNA) for each blastocyst that underwent NGS testing was evaluated, and a significant difference was found between the copy number of mtDNA for the euploid and the chromosomally abnormal blastocysts. So far, out of 42 ongoing pregnancies, 24 babies were born in NGS cycles; all of these babies are healthy and free of any developmental problems. CONCLUSIONS: This study provides the first evaluation of the clinical outcomes of NGS-based pre-implantation genetic diagnosis/screening, and shows the reliability of this method in a clinical and array-based laboratory setting. NGS provides an accurate approach to detect embryonic imbalanced segmental rearrangements, to avoid the potential risks of false signals from SNP array in this study.

A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing.

Copy number variations (CNVs), a common genomic mutation associated with various diseases, are important in research and clinical applications. Whole genome amplification (WGA) and massively parallel sequencing have been applied to single cell CNVs analysis, which provides new insight for the fields of biology and medicine. However, the WGA-induced bias significantly limits sensitivity and specificity for CNVs detection. Addressing these limitations, we developed a practical bioinformatic methodology for CNVs detection at the single cell level using low coverage massively parallel sequencing. This method consists of GC correction for WGA-induced bias removal, binary segmentation algorithm for locating CNVs breakpoints, and dynamic threshold determination for final signals filtering. Afterwards, we evaluated our method with seven test samples using low coverage sequencing (4∼9.5%). Four single-cell samples from peripheral blood, whose karyotypes were confirmed by whole genome sequencing analysis, were acquired. Three other test samples derived from blastocysts whose karyotypes were confirmed by SNP-array analysis were also recruited. The detection results for CNVs of larger than 1 Mb were highly consistent with confirmed results reaching 99.63% sensitivity and 97.71% specificity at base-pair level. Our study demonstrates the potential to overcome WGA-bias and to detect CNVs (>1 Mb) at the single cell level through low coverage massively parallel sequencing. It highlights the potential for CNVs research on single cells or limited DNA samples and may prove as a promising tool for research and clinical applications, such as pre-implantation genetic diagnosis/screening, fetal nucleated red blood cells research and cancer heterogeneity analysis.

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.