APOE genotyping: comparison of three methods

Apolipoprotein E (apo E) polymorphism is associated with increased risk of cardiovascular and Alzheimer diseases, making its genotyping of potentially predictive value. We developed a rapid, reliable and specific method for determining APOE genotypes by fluorescent resonance energy transfer (FRET) over a high number of samples in a single run using a LightTyper device and dedicated probes. The method, validated with 75 blood samples, was designed to simultaneously detect three common APOE polymorphisms, epsilon(2,) epsilon(3) and epsilon(4), and to identify in a single reaction any of the six following genotypes: epsilon(2)/epsilon(2), epsilon(3)/epsilon(3), epsilon(4)/epsilon(4), epsilon(3)/epsilon(4), epsilon(4)/epsilon(2), epsilon(3)/epsilon(2). The assay involved three phases: (1) DNA extraction, (2) amplification, and (3) melting curve analysis using FRET technique. Briefly, genomic DNA of patients was extracted from total blood. Fragment of APOE was amplified by a first PCR run. Fluorescent labeled probes were added in a second PCR run. FRET genotyping showed following distribution: (1) 1.3% for epsilon(2)/epsilon(2) and epsilon(4)/epsilon(4) homozygotes, (2) 4.0, 6.6 and 14.7% for epsilon(2)/epsilon(4), epsilon(2)/epsilon(3) and epsilon(3)/epsilon(4) heterozygotes, respectively, and (3) 72.0% for epsilon(3)/epsilon(3) homozygotes. Moreover, a careful analysis of the FRET melting curves allowed us to determine the presence of a new polymorphism on the third position of the codon 158 (-AAGCGT-), namely, two nucleotides downstream from the known polymorphism. When the FRET analysis was compared to those obtained by RFLP and sequencing, the presence of this new polymorphism was confirmed only by sequencing thus indicating that RFLP analysis is not always reliable for genotyping.     

Direct comparison of hepatitis C virus genotypes tested by INNO-LiPA HCV II and TRUGENE HCV genotyping methods.

BACKGROUND: Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. It is associated with the development of end-stage liver disease and hepatocellular carcinoma. Studies have shown that patients infected with different genotypes of HCV may respond to interferon-ribavirin therapy differently and thus HCV genotype information is very important in helping physicians to better managing their patients. OBJECTIVES: Compare the end results of HCV typing of the two commercially available tests. STUDY DESIGN: TRUGENE Genotyping test (Visible Genetics) was used to analyze clinical specimens obtained from North America. The 5' NC was amplified with the Roche COBAS Amplicor HCV Monitor Test. Amplification products were blinded and genotyped by the TRUGENE HCV 5'NC method. Genotype results were compared with those obtained by the reverse hybridization based INNO-LiPA HCV II (Innogenetics) assay. Additional sequencing of the NS5B region was done to resolve discrepancies. RESULTS AND CONCLUSIONS: Among the total of 110 consecutively collected serum specimens submitted for HCV genotyping, 108/110 could be typed by the sequencing method and 107/110 were typable by LiPA HCV II method. Our experiences with the tests suggest that at type level, HCV genotype results are 100% concordant between the two tests studied for those 106 specimens successfully typed by both methods. More sensitive amplification, such as qualitative PCR, is needed to test specimens with viral load lower than 20000 IU/ml. Both tests can be easily adapted by a clinical diagnostic laboratory.     

Borderline and/or discordant Cobas Amplicor HCV Test version 2.0 results: clinical significance.

BACKGROUND: The Cobas Amplicor HCV Test Version 2.0 (Roche Diagnostics, Mannheim, Germany) allows highly sensitive detection of hepatitis C virus (HCV) RNA in patient samples (> or =100 copies/ml with 100% reproducibility) and yields reproducible, unambiguous results that correlate well with relevant serological and clinical parameters. Occasionally, however, results are borderline (defined by Roche Diagnostics as optical density 0.15-1.0) and/or discordant upon repetition. Such results are difficult to interpret: do they represent false-positives or reflect very low-level viremia (<100 copies/ml)? OBJECTIVE: To determine whether low-level viremia could be a plausible explanation for the borderline/discordant results observed with this test. STUDY DESIGN: (1) Analyse serial dilutions of two HCV standards and one HCV quantitated patient serum; and (2) correlate ambiguous results from 21 patients with available clinical and laboratory data. RESULTS: (1) All dilutions containing >100 copies/ml yielded 100% concordant positive results, whereas dilutions with <100 copies/ml yielded discordant results, often with borderline values. (2) All patients had either a confirmed HCV infection (n=14, seropositive, most undergoing therapy with interferon-alpha) or had a history of confirmed or suspected contact with HCV without confirmed HCV infection (seronegative): three needle-stick injuries, one newborn of an HCV seropositive mother, one woman with liver cirrhosis of unknown etiology, one iv drug abuser, and one nurse with a prior blood transfusion and "indeterminant HCV results" at a blood donation center. CONCLUSION: Based on our experience to date, borderline results and/or discordant replicates obtained with the Cobas Amplicor HCV Test Version 2.0 are indicative of very low level viremia (<100 copies/ml) due either to an HCV infection (patients will be seropositive) or to transient contact with the virus with or without subsequent HCV infection (patients will be seronegative and may remain so). Follow-up of such patients is mandatory.     

Comparison of three HCV genotyping assays: a serological method as a reliable and inexpensive alternative to PCR based assays.

BACKGROUND: Determination of hepatitis C virus (HCV) genotypes and subtypes is of rising clinical importance. In times where also an increasing need for cost effectiveness can be observed, the demand for fast and easy performable assays grows. OBJECTIVES: To evaluate and compare different genotyping methods regarding their reliability, practicability, and expense in the daily routine. METHODS: Sera of 39 patients infected with different HCV subtypes were examined by a serological genotyping assay (NS-4 IBA), by the widely used INNO-LiPA HCV II, and by a nucleotide sequencing method. RESULTS: The tests performed equally well in terms of HCV subtyping and no different results were obtained. However, the serotyping assay provided the results in less than half the time needed by the other two assays. Significant differences were also observed regarding the 'hands on' times and the costs. The technical equipment which was necessary to perform the assays is significantly reduced using the serological assay. CONCLUSION: Our study demonstrates that the serological test offers the opportunity to determine HCV genotypes and subtypes reliably, fast, easy, and cost effective.     

探讨三种检测方法在丙型肝炎诊断中的应用价值

目的探讨ELISA法检测丙型肝炎病毒核心抗原(HCVcAg)、病毒抗体(抗-HCV)及RT-PCR法检测丙型肝炎病毒RNA(HCV-RNA)3种方法在丙型肝炎诊断的应用价值。方法采用HCVcAg ELISA试剂盒,抗-HCV ELISA试剂盒及HCV-RNA PCR试剂盒,对临床200例疑似丙肝病毒感染的样本进行HCVcAg、抗-HCV和HCV-RNA检测。结果 HCVcAg阳性检出率为42%;HCV-RNA阳性检出率最高,为61%;抗-HCV阳性检出率为52%。Kappa检验示3种检测方法结果阳性吻合度基本一致。HCVcAg阳性检出率随着HCV病毒含量的升高而升高。结论 3种方法中,RT-PCR检测HCV-RNA仍是判断丙肝感染最准确方法。HCV核心抗原检测可以有效缩短窗口期,联合运用抗-HCV和HCVcAg或抗-HCV和HCV-RNA,能有效降低单独使用抗-HCV检测的漏检风险。HCVcAg可作为HCV抗体常规检测的补充指标,提高检出率。     

Comparison of three methods for genotyping of prothrombotic polymorphisms

Several methods have been developed to detect common prothrombotic mutations, including factor V Leiden (G1691), prothrombin G20210A, and methylenetetrahydrofolate reductase (MTHFR) C677C. In this study, we compared the accuracy of three different molecular techniques, i.e.: (1) restriction enzyme digestion (RFLP), (2) real time with hybridization probes and final melting curve (Fluorescence Resonance Energy Transfer, FRET), and (3) real time with hydrolysis probes (TaqMan^®). Sequencing was used as the reference standard. Our data showed that RFLPs analysis for the detection of prothrombotic mutations, albeit easy-to-perform, had a limited reliability for assessing correct genotypes. FRET analysis displayed higher resolution than RFLPs. Additionally, FRET analysis was faster and less tedious than sequencing.     

Cherchez la femme: maternal incidental findings can explain discordant prenatal cell-free DNA sequencing results

Circulating DNA fragments in a pregnant woman’s plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy. Similarly, maternal tumors, both benign and malignant, can release DNA fragments that contain duplications or deletions. Bioinformatics algorithms can subsequently interpret the raw sequencing data incorrectly, resulting in false-positive test reports of fetal monosomies or test failures. Maternal sex-chromosome abnormalities, both constitutional and somatic, can generate results that are discordant with fetal ultrasound examination or karyotype. Maternal copy-number variants and mosaicism for autosomal aneuploidies can also skew interpretation. A maternal etiology should therefore be considered in the differential diagnosis of prenatal cell-free DNA test failures, false-positive and false-negative sequencing results. Further study is needed regarding the clinical utility of reporting maternal incidental findings.     

Comparison of different HCV viral load and genotyping assays.

BACKGROUND: We report an interlaboratory comparison of methods for the determination of hepatitis C virus (HCV) serum load and genotype between a recently, established molecular laboratory at the Alaska Native Medical Center (ANMC) and two independent laboratories using different assays. At ANMC, a Real-time quantitative RT-PCR amplification methodology (QPCR) has been developed in which HCV viral loads are determined by interpolation of QPCR results to those of standards calibrated to the World Health Organization (WHO) First International Standard for HCV. HCV genotype is subsequently determined by direct sequencing of the DNA fragment generated from the QPCR assay. OBJECTIVES AND STUDY DESIGN: The above methods were statistically compared to results obtained for the same patient sera by two independent laboratories using different commercially available viral load assays; Quantiplex HCV RNA (Bayer Diagnostics) and Amplicor HCV Monitor (v 2.0) (Roche Molecular Systems), as well as two different genotyping assays; restriction fragment length polymorphism (RFLP) and INNO-LiPA HCV II (Innogenetics). RESULTS: ANMC's Real-time QPCR HCV viral load results compared moderately well with those obtained by the Quantiplex HCV RNA method (R2=0.3813), and compared quite well with recent lot numbers of Amplicor HCV Monitor in which viral loads are derived in IU/ml (R2=0.6408), but compared poorly with earlier lot numbers of Amplicor HCV Monitor in which viral loads were derived in copies/ml (R2=0.0913). The ANMC direct sequencing method for genotype determination compared moderately to very well with both the RFLP (84-86%) and INNO-LiPA (85-97.5%) methods. CONCLUSIONS: These viral load comparisons highlight the discrepancies that may occur when patient HCV viral loads are monitored using different types of assays. Comparison of HCV genotype by different methods is more reliable statistically and important clinically for predicting probability of response to antiviral therapy. However, viral loads are important for monitoring response once therapy has begun.     

三种测序DNA模板制备方法的比较○

背景：DNA模板质量对DNA序列测定起着至关重要的作用。 目的：为基因组DNA或甲基化DNA测序寻找一种经济,简便的方法。 方法：分别采用96管集合板及96孔板提取质粒,并且针对质粒设计一对包含目的片段的引物,扩增后纯化PCR产物,通过以上3种方法制备DNA测序模板进行测序。 结果与结论：实验所采用的3种方法对于基因组DNA测序效果无差异(P > 0.05)。对于甲基化DNA测序效果,96管集合板法优于其他2种方法(P < 0.05)。说明3种方法均适用于基因组DNA的测序,而96管集合板法更适用于甲基化DNA的测序。      

中国人群HCV精确基因分型和新亚型的鉴定

<正>1研究背景和目的:丙型肝炎病毒(HCV)非结构蛋白5B(NS5B)区域核苷酸测序是HCV基因分型的金标准。本文拟建立一种新的NS5B区域核苷酸测序方法,并对该方法能否增加HCV基因测序的准确性和灵敏度进行评估。2方法:从HCV数据库中提取HCV基因组序列,采用BLAST分析序列的相似性,利用Primer5.0等引物设计软件设计所有可能的PCR扩增引物,通过进化树分析所扩增片段的分型能力。利用设计的引物检测HCV感染人群,分析其对HCV的分型能力。     

Comparative study of three methods for genotyping hepatitis C virus strains in samples from Spanish patients.

Hepatitis C virus (HCV) genotypes may be investigated by a variety of laboratory methods that target different parts of the HCV genome and have various degrees of technical difficulty. Since the choice of a particular method is difficult, we compared the performance of (i) a type-specific PCR with type-specific primers from the core region, (ii) molecular hybridization of the PCR-amplified 5' noncoding region to type-specific probes, and (iii) identification of type-specific antibodies against epitopes of nonstructural region 4 by enzyme-linked immunosorbent assay (ELISA). One hundred fifty-one patients with biopsy-proved chronic hepatitis and HCV RNA in serum were investigated. The HCV genotype was identified in 99%, 100%, and 85% of the cases by type-specific PCR, probe hybridization, and ELISA, respectively. The type-specific PCR disclosed infection with type 1a in 3%, type 1b in 74%, and type 3a in 4% of the cases and suggested infection with two or more HCV types, including 2a/2c and 2b, in the remaining 18%. Apparently mixed infections were more prevalent in patients with past intravenous drug use (P < 0.001), but cloning and sequencing of PCR products did not confirm a mixed infection in any of the four cases investigated. Concordant results were obtained by the three procedures with virtually all of the samples in which the type-specific PCR revealed a single HCV genotype. Type-specific hybridization and ELISA usually recognized the genotype producing the strongest DNA band in samples in which type-specific PCR suggested a mixed infection. In conclusion, the three procedures evaluated in this study are reliable for investigation of HCV genotype. Type-specific PCR provides information about HCV subtypes, but a mixed infection detected with this method should be interpreted with caution.     

Improved accuracy of clinical HLA genotyping by next-generation DNA sequencing affects unrelated donor search results for hematopoietic stem cell transplantation

Matching of human leukocyte antigen (HLA) genes is critically important in hematopoietic stem cell transplantation (HSCT). HLA genes are highly polymorphic and HLA matching has historically been limited by technologies that are unable to unambiguously determine HLA genotypes. Next generation DNA sequencing (NGS) overcomes these limitations by enabling near full-gene sequences with phase determination for heterozygous alleles. Here we examine the efficacy and utility of HLA-NGS in the clinical setting. In a 54-sample validation study and 955 patient samples subsequently tested using HLA-NGS, we observed significant improvement in the ability to unambiguously identify HLA genotypes in both the validation (97.3%) and clinical (97.4%) sample cohorts compared to previous standard-of care HLA genotyping methods. We modeled the clinical impact of this improved diagnostic ability by comparing National Marrow Donor Program (NMDP) search results for 56 patients using HLA-NGS genotypes and simulated standard-of-care HLA genotypes. Surprisingly, we observed significant differences in 7.1% of NMDP searches, with improved unambiguous HLA genotyping correlating with improved prediction of finding well-matched and partially-matched unrelated HSCT donors. These data demonstrate that HLA-NGS can provide highly accurate and unambiguous HLA genotyping that facilitates donor selection for allogeneic HSCT.     

Clinical evaluation of two methods for genotyping hepatitis C virus based on analysis of the 5' noncoding region

We compared the performance characteristics of a standardized direct sequencing method (TRUGENE HCV 5'NC; Visible Genetics Inc., Toronto, Ontario, Canada) and a reverse hybridization line probe assay (INNO-LiPA HCV II; Bayer Corp., Tarrytown, N.Y.) for genotyping of hepatitis C virus (HCV). Both methods are based on detection of sequence heterogeneity in the 5' noncoding (5'NC) region. Concordance between the genotyping methods was assessed by testing 172 samples representing the six major genotypes. Sequence analysis of the more phylogenetically informative nonstructural 5B (NS5B) region was also done with 148 (86%) samples to confirm the accuracy of and resolve discrepancies between the 5'NC genotyping results. The sensitivities of the methods were assessed by using the 5'NC amplicon from both the qualitative and quantitative AMPLICOR HCV tests (Roche Diagnostics Corp., Indianapolis, Ind.). The ability of the methods to detect mixed-genotype infections was determined with mixtures of two different genotypes at relative concentrations ranging from 1 to 50%. Both 5'NC methods were able to genotype 99.4% of the samples with type agreement for 99.5% and subtype agreement for 68.2% of the samples. No or ambiguous subtype results were found by the line probe assay for 16.5% and by the TRUGENE 5'NC test for 17.1% of the samples. Discrepancies occurred between the line probe assay and NS5B results at the type level for 1.4% of the samples and at the subtype level for 14.2% of the samples. Discrepancies also occurred between the TRUGENE 5'NC and NS5B results at the type level for 2% of the samples and at the subtype level for 8.1% of the samples. We also found two distinct strains of HCV classified as type 2 by analysis of the 5'NC region that were type 1 by analysis of the NS5B region. The sensitivities of the two 5'NC genotyping methods were comparable and dependent on the amplification test used ( approximately 10(3) IU/ml with the qualitative HCV RNA tests and approximately 10(5) IU/ml with the quantitative HCV RNA tests). Genotype mixtures were successfully identified at a relative concentration of 5% by the line probe assay and 10% by the TRUGENE 5'NC test. In conclusion, the performance characteristics of the 5'NC methods were similar and both methods produced accurate results at the genotype level but neither method should be used for subtyping.     

Analysis of hepatitis B virus genotyping and drug resistance gene mutations based on massively parallel sequencing

Drug resistance to nucleoside analogs is a serious problem worldwide. Both drug resistance gene mutation detection and HBV genotyping are helpful for guiding clinical treatment. Total HBV DNA from 395 patients who were treated with single or multiple drugs including Lamivudine, Adefovir, Entecavir, Telbivudine, Tenofovir and Emtricitabine were sequenced using the HiSeq 2000 sequencing system and validated using the 3730 sequencing system. In addition, a mixed sample of HBV plasmid DNA was used to determine the cutoff value for HiSeq-sequencing, and 52 of the 395 samples were sequenced three times to evaluate the repeatability and stability of this technology. Of the 395 samples sequenced using both HiSeq and 3730 sequencing, the results from 346 were consistent, and the results from 49 were inconsistent. Among the 49 inconsistent results, 13 samples were detected as drug-resistance-positive using HiSeq but negative using 3730, and the other 36 samples showed a higher number of drug-resistance-positive gene mutations using HiSeq 2000 than using 3730. Gene mutations had an apparent frequency of 1% as assessed by the plasmid testing. Therefore, a 1% cutoff value was adopted. Furthermore, the experiment was repeated three times, and the same results were obtained in 49/52 samples using the HiSeq sequencing system. HiSeq sequencing can be used to analyze HBV gene mutations with high sensitivity, high fidelity, high throughput and automation and is a potential method for hepatitis B virus gene mutation detection and genotyping.     

HLA-DQA1 genotyping by bi-directional sequencing of PCR-amplified DNA spanning exon 2

We describe a simple, reliable technique for HLA-DQA1 genotyping based on direct DNA sequencing of PCR amplified fragments from genomic DNA. The alleles of DQA1 can be divided into two subsets, with one subset demonstrating a 3 base deletion in exon 2 relative to the other. Typing heterozygous individuals who possess one allele from each sub-group can be difficult using a direct sequencing approach, since the two overlapping DNA sequences move out of phase by 3 nucleotides once the point of deletion is reached. The complete sequence is obtained by performing two separate sequencing reactions with fluorescent dye primers, coming from either end of the template. This allows all heterozygous positions in exon 2 to be unambiguously assigned.     

Successful HCV genotyping of previously failed and low viral load specimens using an HCV RNA qualitative assay based on transcription-mediated amplification in conjunction with the line probe assay.

BACKGROUND: Hepatitis C virus (HCV) genotyping is a critical part of the diagnostic work-up for chronic hepatitis C. The VERSANT HCV line probe assay (LiPA) marketed by Bayer Corporation requires PCR-derived amplicons for genotyping usually obtained from commercial assays, including Amplicor HCV 2.0 (Amplicor 2.0), Amplicor HCV Monitor 2.0, or SuperQuant. Occasionally, PCR-based methods in conjunction with LiPA fail to give a genotyping result. Although most genotyping failures occur among low viral load specimens, some occur in specimens with relatively high viral loads. The Bayer HCV RNA Qualitative assay (HCV TMA), with a limit of detection of approximately 5-10 IU/ml, is more sensitive than other commercial assays. OBJECTIVES: An HCV genotyping protocol using HCV TMA linked with LiPA (TMA-LiPA) was developed and tested for ability to genotype samples that had previously failed genotyping by PCR-based methods in conjunction with LiPA. STUDY DESIGN: Clinical specimens were obtained from eight independent laboratories in Canada and the US and tested with TMA-LiPA at the Bayer Reference Testing Laboratory. Specimens included those that failed to produce a genotype result when a PCR-based assay was used in conjunction with LiPA and specimens for which genotyping was not attempted because the viral load was below the validated cut-off determined in the laboratory of origin. RESULTS AND CONCLUSIONS: TMA-LiPA successfully genotyped 68 of 75 (90.7%) specimens that had failed genotyping by PCR-based methods used in conjunction with LiPA and 36 of 40 (90.0%) specimens that were rejected for genotyping due to low viral load. Moreover, TMA-LiPA assigned subtype for 79 of 107 (73.8%) specimens. Our TMA-LiPA results reflected the distribution of HCV genotypes found in North America, and were 100% concordant with those of Amplicor 2.0 in conjunction with LiPA for control specimens genotyped by both assays. TMA-LiPA may prove useful both in optimizing LiPA performance and genotyping patient specimens.     

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing

Massively parallel DNA sequencing technologies have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods have been developed to enrich for genomic regions of interest for targeted sequencing. We have compared three of these methods: Molecular Inversion Probes (MIP), Solution Hybrid Selection (SHS), and Microarray-based Genomic Selection (MGS). Using HapMap DNA samples, we compared each of these methods with respect to their ability to capture an identical set of exons and evolutionarily conserved regions associated with 528 genes (2.61 Mb). For sequence analysis, we developed and used a novel Bayesian genotype-assigning algorithm, Most Probable Genotype (MPG). All three capture methods were effective, but sensitivities (percentage of targeted bases associated with high-quality genotypes) varied for an equivalent amount of pass-filtered sequence: for example, 70% (MIP), 84% (SHS), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of >99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and >99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods; of the heterozygous positions identified by each of the capture methods, >99.57% agreed with 1M SNP BeadChip, and >98.840% agreed with the whole-genome shotgun data. In addition, we successfully piloted the genomic enrichment of a set of 12 pooled samples via the MGS method using molecular bar codes. We find that these three genomic enrichment methods are highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data.The ability to identify genetic alterations underlying disease and phenotypic variation is a major goal of the ongoing genomics revolution. Large-scale medical sequencing holds the promise of elucidating the genetic architecture of virtually all diseases, including the relative role of rare and common genetic variants. Such information should inform our understanding of the pathways involved in disease pathogenesis. Additionally, the ability to apply variant discovery to other organisms with annotated genomes is also of great value. So-called next-generation DNA sequencing technologies that involve massively parallel clonal ensemble sequencing are creating new opportunities for comprehensive genomic interrogation, bypassing some of the limitations associated with high-throughput electrophoresis-based sequencing methods (Margulies et al. 2005; Shendure et al. 2005; Bentley et al. 2008). Although advances in these new technologies are being made at a rapid pace, the cost of sequencing a whole human genome and the associated costs and technical hurdles of data storage and analysis remain high for most large projects. As a result, methods are needed for efficient comprehensive sequencing of targeted genomic regions.A number of genomic enrichment (or targeted capture) methods have been developed and used with varying levels of success (for reviews, see Garber 2008; Summerer 2009; Turner et al. 2009b; Mamanova et al. 2010). Not surprisingly, each method has both common and unique issues related to the required input DNA, specificity and coverage, sensitivity and accuracy, scalability and potential for automation, and cost-effectiveness. Although multiple publications describe the individual methods (Albert et al. 2007; Hodges et al. 2007; Okou et al. 2007; Porreca et al. 2007; Craig et al. 2008; Krishnakumar et al. 2008; Bau et al. 2009; Gnirke et al. 2009; Herman et al. 2009; Hodges et al. 2009; Li et al. 2009; Summerer et al. 2009; Tewhey et al. 2009), numerous variables are inherent to each experiment, including the nature of the targeted genomic region(s), sequencing platform, analysis software, and performance metrics; these variables make objective comparisons of the different methods challenging to perform.Here, we report the testing, optimizing, and rigorous comparing of three genomic enrichment methods: Molecular Inversion Probes (MIP) (Porreca et al. 2007), Solution Hybrid Selection (SHS; Agilent) (Gnirke et al. 2009), and Microarray-based Genomic Selection (MGS; Roche-NimbleGen) (Albert et al. 2007; Okou et al. 2007). All three methods were tested for their ability to capture the same 2.61 Mb of noncontiguous DNA sequence from an overlapping set of two HapMap DNA samples. We also report, for the first time, a novel Bayesian genotype-assigning algorithm, Most Probable Genotype (MPG), which was used to analyze the sequence data from all three capture methods. Furthermore, we introduce a pre-capture bar-coding strategy to allow pooling of samples for capture and sequencing. In contrast to previous reviews of genomic enrichment methods, we have directly compared these methods by evaluating genotype sensitivity and accuracy of variant detection, providing insights about overall performance and relative costs.     

基因芯片在丙型肝炎病毒分型检测中的评价

为研究HCV基因分型芯片检测丙型肝炎患者的基因型,以测序法进行对比,并探讨了IFN治疗慢性丙肝疗效与基因型的关系。采用基因芯片的方法对20例慢性丙型肝炎患者进行分型,并通过测序验证。结果基因芯片和测序结果完全一致。20例丙肝患者中18例为1b,2例为2a,并且IFN治疗效果2a较1b型为优。HCV分型芯片检测HCV分型,特异性强、灵敏度高、结果准确,支持HCVRNA基因型在评价IFN疗效中十分重要的观点。