Preimplantation High-Resolution HLA Sequencing Using Next Generation Sequencing

Hematopoietic stem cell transplantation (SCT) is the only therapeutic option in a number of heritable hematologic disorders and hematologic cancers. Many parents and families fail to find an HLA-identical donor for their affected family member. In such cases, conceiving for a “savior baby” remains the only option, especially in countries without access to national registries. By means of next generation sequencing (NGS) techniques, in a single experiment on single-cell products of in vitro fertilization, a healthy HLA-identical embryo can be implanted in the uterus of a concerned mother. The patient can therefore benefit from cord blood SCT along with confirming that the fetuses are not suffering from the heritable disorder. This study is an attempt to study the feasibility of preimplantation HLA sequencing on single blastomeres using NGS. Two couples who had previously undergone preimplantation genetic diagnosis of β-thalassemia and their overall 10 embryos were studied and their 5 HLA loci were typed in high resolution through multiple displacement amplification and NGS of single cells. For 88.9% of the 90 HLA alleles, conclusive HLA typing in 4 digit sets was made. HLA alleles were typed; 1 ambiguity in the allelic group and 4 ambiguities in the protein level were observed that were then unraveled by haplotype analysis. Amplification efficiency was 93.3% with an allele drop-out (ADO) rate of 22.2% (6 alleles dropped from a maximum of 27 possible ADOs). In this study the feasibility of a new method of preimplantation HLA sequencing via combining the state-of-the-art techniques used in single-cell whole genome amplification, preimplantation genetic diagnosis, and high-resolution HLA typing by NGS has been shown. This method can make preimplantation HLA sequencing a practicable technique in families desperate for an HLA-matched donor.     

新一代DNA测序技术

近年来新型DNA测序平台454、Solexa、SOLiD、Polonator和HeliSeope等得到迅速推广,使测序成本下降了2-3个数量级.原先只能由大型测序中心完成的基因组项目,现在已经可以在个人实验室中实现.这些新技术大大加速了生物医学的研究步伐,因为全面分析基因组、转录物组和代谢组已不再是高不可攀,而将成为广泛运用的常规分析.本文介绍DNA测序新技术的原理、特点、现状和应用前景.     

新一代DNA测序技术

近年来新型DNA测序平台454、Solexa、SOLiD、Polonator和HeliSeope等得到迅速推广,使测序成本下降了2-3个数量级.原先只能由大型测序中心完成的基因组项目,现在已经可以在个人实验室中实现.这些新技术大大加速了生物医学的研究步伐,因为全面分析基因组、转录物组和代谢组已不再是高不可攀,而将成为广泛运用的常规分析.本文介绍DNA测序新技术的原理、特点、现状和应用前景.     

Targeted Next‐Generation Sequencing can Replace Sanger Sequencing in Clinical Diagnostics

Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted next‐generation sequencing (NGS), in which a selected fraction of genes is sequenced, may circumvent these shortcomings. We aimed to determine whether the sensitivity and specificity of targeted NGS is equal to those of SS. We constructed a targeted enrichment kit that includes 48 genes associated with hereditary cardiomyopathies. In total, 84 individuals with cardiomyopathies were sequenced using 151 bp paired‐end reads on an Illumina MiSeq sequencer. The reproducibility was tested by repeating the entire procedure for five patients. The coverage of ≥30 reads per nucleotide, our major quality criterion, was 99% and in total ～21,000 variants were identified. Confirmation with SS was performed for 168 variants (155 substitutions, 13 indels). All were confirmed, including a deletion of 18 bp and an insertion of 6 bp. The reproducibility was nearly 100%. We demonstrate that targeted NGS of a disease‐specific subset of genes is equal to the quality of SS and it can therefore be reliably implemented as a stand‐alone diagnostic test.     

Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus

spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an in-house analysis pipeline determines the spa types. Due to national surveillance, all MRSA isolates are sent to Statens Serum Institut, where the spa type is determined by PCR and Sanger sequencing. The purpose of this study was to evaluate the reliability of the spa types obtained by 150-bp paired-end Illumina WGS. MRSA isolates from new MRSA patients in 2013 (n = 699) in the capital region of Denmark were included. We found a 97% agreement between spa types obtained by the two methods. All isolates achieved a spa type by both methods. Nineteen isolates differed in spa types by the two methods, in most cases due to the lack of 24-bp repeats in the whole-genome-sequenced isolates. These related but incorrect spa types should have no consequence in outbreak investigations, since all epidemiologically linked isolates, regardless of spa type, will be included in the single nucleotide polymorphism (SNP) analysis. This will reveal the close relatedness of the spa types. In conclusion, our data show that WGS is a reliable method to determine the spa type of MRSA.     

Sequencing needs for viral diagnostics

We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (near neighbors) that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near-neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near-neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. Severe acute respiratory syndrome and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near-neighbor sequences are urgently needed. Our results also indicate that double-stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.     

Antiretroviral therapy. Sequencing antiretrovirals

Sequencing of antiretroviral agents is of interest because the majority of HIV-infected individuals in clinical practice experience virologic rebound after 1 to 2 years of therapy. Sequencing strategies are based on the observation that different mutational patterns arise after exposure to particular antiretroviral agents within the same class and on preliminary data suggesting that not all mutations impart the same degree of cross-resistance to other agents of the same class. The ultimate goal of sequencing is to maximize the number of effective antiretroviral combinations available. While convincing data on the efficacy of sequencing strategies from large, randomized clinical trials are lacking, early data suggest that some sequencing strategies may be of benefit.     

Metagenomic Next-Generation Sequencing in Clinical Microbiology

Identification of causative pathogens in infectious disease is a critical component of health care, as infectious diseases continue to be a leading cause of mortality and morbidity worldwide. In addition, the detection of drug resistance by traditional and novel antimicrobial susceptibility testing methods is becoming ever more important as antimicrobial resistance continues to emerge and spread. While culture-based methods are the current reference standard for identifying microbes, the time required to achieve results and the difficulty in culturing certain fastidious organisms have led to the development of multiple alternatives. Alternatives to culture, such as polymerase chain reaction (PCR) assays, serologic assays, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and 16S rRNA gene sequencing have been used in clinical laboratories, and positive impacts on patient care have been documented. Nonetheless, such methods require either presumption about the type of microbes present in the sample or growth of the organism(s) before analysis. Subsequently, there are some documented limitations in the routine detection methods for clinically relevant organisms.In contrast to the routine alternatives listed above, modern nucleic acid sequencing platforms support sequencing of random DNA strands, an approach known as “shotgun” sequencing of the DNA, also known as metagenomic next-generation sequencing (mNGS) present in the sample. The mNGS approach offers an unbiased and hypothesis-free approach to pathogen identification with the future potential to (i) achieve results in 12 to 24 hours; (ii) avoid the challenges associated with growth of fastidious organisms; (iii) avoid the biased growth that occurs when only routine culture medium is used; (iv) detect viral, fungal, and parasitic organisms in the same assay; and (v) detect the presence of drug resistance genes. Advances in mNGS technology and data analysis have reduced testing costs to the point where the potential advantages of mNGS over culture and other methods warrant its development for use in clinical settings. In this review, the mNGS approach is discussed, along with a comparison to other methods, limitations, and suggestions for further development and overcoming hurdles to adoption in the clinical setting.     

Toward Real-World Sequencing by Microdevice Electrophoresis

We report results using a microdevice for DNA sequencing using samples from chromosome 17, obtained from the Whitehead Institute Center for Genome Research (WICGR) production line. The device had an effective separation distance of 11.5 cm and a lithographically defined injection width of 150 microm. The four-color raw data were processed, base-called by the sequencing software Trout, and compared to the corresponding ABI 377 sequence from WICGR. With a criteria of 99% accuracy, we achieved average continuous reads of 505 bases in 27 min with 3% linear polyacrylamide (LPA) at 150 V/cm, and 460 bases in 22 min with 4% LPA at 200 V/cm at a temperature of 45 degrees C. In the best case, up to 565 bases could be base-called with the same accuracy in <25 min. In some instances, Trout allowed for accurate base-calling down to a resolution R as low as R = 0.35. This may be due in part to the high signal-to-noise ratio of the microdevice. Unlike many results reported on capillary machines, no additional sample cleanup other than ethanol precipitation was required. In addition, DNA fragment biasing (i.e., discrimination against larger fragments) was reduced significantly through the unique sample injection mechanism of the microfabricated device. This led to increased signal strength for long fragments, which is of great importance for the high performance of the microdevice.     

High-Throughput Plasmid Purification for Capillary Sequencing

The need for expeditious and inexpensive methods for high-throughput DNA sequencing has been highlighted by the accelerated pace of genome DNA sequencing over the past year. At the Joint Genome Institute, the throughput in terms of high-quality bases per day has increased over 20-fold during the past 18 mo, reaching an average of 18.3 million bases per day. To support this unprecedented scaleup, we developed an inexpensive automated method for the isolation and purification of double-stranded plasmid DNA clones for sequencing that is tailored to meet the more stringent needs of the newer capillary electrophoresis DNA sequencing machines. The protocol is based on the magnetic bead method of solid phase reversible immobilization that has been automated by using a CRS-based robotic system. The method described here has enabled us to meet our increases in production while reducing labor and materials costs significantly.     

Pitfalls and Caveats in BRCA Sequencing

Between 5 and 10% of breast cancer cases are considered to result from hereditary predisposition. Germ-line mutations in BRCA1 and BRCA2 are responsible for an inherited predisposition of breast and ovarian cancer. Direct nucleotide sequencing is considered the gold standard technique for mutation detection for genes such as BRCA1 and BRCA2. In many laboratories that analyze BRCA1 and BRCA2, previous to direct sequencing, screening techniques to identify sequence variants in the PCR amplicons are performed. The mutations detected in these genes may be frameshift mutations (insertions or deletions), nonsense mutations, or missense mutations. The clinical interpretation of the mutation as the cause of the disease may be difficult to establish in the case of missense mutations. Only in 30–70% of the families in which a hereditary component is suspected, a mutation in BRCA1 and/or BRCA2 is detected. Negative results may be due to: wrong selection of the proband; mutations in the regulatory portion of the genes; gene silencing due to epigenetic phenomena; or large genomic rearrangements that produce deletions of whole exons. Another possibility that explains the lack of detection of alterations in BRCA1 or BRCA2 is the presence of mutations in undiscovered genes or in genes that interact with BRCA1 and/or BRCA2, which may be low-penetrance genes, like CHEK2.     

Sequencing of 15 new BoLA-DRB3 alleles

The class II DR of bovine major histocompatibility complex of cattle (BoLA) plays a central role in the regulation of the immune response through their ability to present those peptides to T-cell receptors. In this work, we sequenced the exon2 of DRB3 to identify new alleles in Chinese yellow cattle, a total of 15 new BoLA-DRB3 alleles were found.     

Principles of Capillary-Based Sequencing for Clinical Microbiologists

Chain termination cycle sequencing, or “first-generation” DNA sequencing, was developed 3 decades ago but remains one of the most commonly used procedures for diagnostic analyses. Automated capillary-gel electrophoresis genetic analyzers greatly improved the efficiency of sequencing DNA templates between 100 and approximately 1,300 nucleotides long. Cycle sequencing may be completed the same day by using fast protocols for the initial amplification and cycle-sequencing reactions and by utilization of commercial sequence interpretation and analysis software. These changes allowed sequencing to become a routine tool for pathogen identification, discovery, and genotyping.