Instrument Illumina Research Articles

Pooling HLA, chimerism, and cfDNA NGS libraries for sequencing on illumina instruments

Pooling HLA, chimerism, and cfDNA NGS libraries for sequencing on illumina instruments

Multi-center evaluation of 19 loci hybrid capture NGS assay on illumina instruments

Multi-center evaluation of 19 loci hybrid capture NGS assay on illumina instruments

B-016 Automated Next Generation Sequencing Fluidic-Based Device for Sample to Library Preparation: A Flexible Solution for Rapid Decentralized Sequencing for Infectious Disease Diagnostics

Abstract Background In addition to the established use of Next Generation Sequencing (NGS), such as drug resistance monitoring in HIV, the recent COVID19 pandemic has shown the crucial need of NGS technologies as tools for identification of clinically relevant variants of the SARS-CoV-2 virus. Typically, in these settings, to be cost-effective most NGS analyses were conducted using larger batch sizes often resulting in long turn-around times of 2–3 weeks the need of trained personnel, and centralized testing facilities. Methods We have developed an easy to use automated fluidic-based benchtop device to bridge a perceived gap in NGS library preparation and provide a solution for decentralized testing that does not require specially trained personnel. With a batch size of 6, smaller hospitals and laboratories can perform NGS library preparation on fresh or archived samples with a fast turn-around-time of two days, facilitating earlier reporting to speed up diagnosis and treatment. The Helaxy NGS fluidic device performs sample nucleic acid extraction and a 2-step PCR in a plastic fluidic card, which is the sole consumable required for the extraction and library prep process.The sample is applied to the fluidic card by manual pipetting followed by loading of the card into the device. Nucleic acids are extracted with a combination of magnetic bead pull-down and centrifugal force in a purification chamber to give an eluate that is spun to a separate PCR chamber that uses the concept of thermal induction and cycling. Barcoding for library preparation follows within the same PCR chamber and the resulting product is transferred into another fluidic card for size selection purification, normalization and pooling to generate a library for input into compatible NGS sequencers, e.g., but not confined to, Illumina instruments. Results In order to demonstrate clinical utility we have shown that the Helaxy NGS fluidic device can successfully extract nucleic acid from at least three sample types: SARS-CoV-2 RNA from nasopharyngeal swabs, HIV RNA from plasma and 16S RNA from stools. Using in-house and commercial assays, we have generated libraries of target amplicons using the fluidic device workflow followed by sequencing with Illumina sequencers iSeq and MiSeq. Sequencing results analysed and reported by the Helaxy NGS Bioinformatics Reporting Pipeline revealed expected variants and mutations in the samples. We correctly identified all the unique mutations such as L211del and G446S in commercially available inactivated Omicron BA1 variant of the SARS-CoV-2 virus as well as characterised drug-resistant mutations such as L90M in the Protease gene and D67N and Y181C in the Reverse Transcriptase gene in commercially available inactivated HIV-1 virus. Conclusion The Helaxy NGS fluidic device can thus effectively provide an easy-to-use automated solution for sample library preparation in decentralized facilities to reduce the turn-around-time from sample collection to result reporting for clinical diagnosis and treatment.

EP158: The utility of transcriptomics to increase diagnostic yield in cases of rare genetic disease

Rare diseases affect less than 1 in 200,000 individuals by definition, however, collectively are common, with approximately 30 million individuals in the United States impacted. Frequently individuals experience an arduous journey towards a rare disease diagnosis, often termed a “diagnostic odyssey”. Exome sequencing (ES) has become standard of care for patients with suspected rare genetic disease, with a diagnostic yield of 30%. Here we report on preliminary results of the largest study to date integrating transcriptome sequencing (RNAseq) with ES to increase diagnostic yield for rare disease patients. A cohort of 406 patients who were consented into the Mayo Clinic Diagnostic Odyssey study were selected for study. All patients had received clinical or research exome sequencing which failed to result in a definitive diagnosis. RNA was extracted from whole blood collected in PAXgene tubes, and sequencing libraries prepared using a hybridization capture protocol with the TruSeq RNA Access Library Prep Kit (Illumina, San Diego, CA). Paired-end 101-basepair reads were sequenced using Illumina instruments. Resulting RNA sequences were analyzed for fusion using two algorithms, LeafCutterMD and Fraser, with results integrated for review. Allele specific expression was determined using AnevaDot. Gene expression was analyzed for outlier expression patterns in individual patients compared to the entire cohort using Outrider. Fusion analysis was performed using an internal workflow previously described. The major advantages RNAseq in addition to ES are the high-throughput functional characterization of DNA variation and the detection of aberrations not identifiable by ES sequencing alone. Recent work has shown a 7.5-35% yield using RNAseq in unsolved rare disease cases, dependent on tissue and methodology. In this study RNAseq was performed on blood from 406 individuals with suspected rare genetic disease for whom clinical ES was non-diagnostic. The transcriptome data was analyzed to interrogate four different effects: genes with outlier expression, aberrant RNA-splicing, gene fusions, and allele specific expression. Splicing analysis utilized two complementary algorithms, FRASER and LeafcutterMD, to identify modified intron usage, shifted splice donor and acceptor sites, intron retention events, and creation of cryptic exons. All data were studied for ultra-rare modifications with potential disease ramifications, using the remaining patient cohort as a control RNASeq population. Our preliminary results include gene fusion events, splice site variants with confirmed splicing alterations, and significantly altered outlier gene expression which were integral to the patient’s genetic diagnosis. RNA sequencing is complementary to DNA sequencing in the search for genetic diagnoses in Mendelian disease. When analyzing RNA data, care must be taken to evaluate all forms of RNA mediated events to obtain a thorough representation of the underlying genetics. Here we discuss a 406 patient cohort study using RNA and DNA sequencing to profile patient seen at the Mayo Clinic. Complete results of this study will provide valuable information regarding the clinical utility of RNAseq in tandem with ES for identifying a genetic diagnosis for rare disease patients.

993. A CRISPR-Powered Universal Infectious Disease Assay

BackgroundThe COVID-19 pandemic has brought awareness to the dangers of emerging pathogens to global human health and welfare. Sensitivity and flexibility are important features for methods used to detect emerging pathogens. While PCR testing is rapid and sensitive, a significant advantage next generation sequencing (NGS) approaches have over PCR-based analyses is the ability to detect previously undiscovered pathogens while also providing genomic information that can detect SARS-CoV-2 genome sequence, identify source of co-infection, and the host transcriptional response in a single workflow. The critical component enabling this approach is Jumpcode CRISPRclean technology which removes abundant human and bacterial ribosomal RNA sequences from NGS libraries.CRISPRclean workflow easily integrates into next generation sequencing projects Schematic of the Jumpcode CRISPRclean protocolMethodsCRISPRclean was applied to contrived infected tissue samples including human lung RNA spiked with serially diluted amounts of SARS-CoV-2 RNA and bacterial RNA. NEB RNA libraries were prepared and treated with CRISPRclean protocol, then sequenced on Illumina instruments. Data analysis was performed using Jumpcode proprietary software to measure alignment and depletion rates, the Silva database for rRNA read alignment, and Kraken2 and CosmosID pipelines for k-mer based metagenomic investigation. Fold enrichment of SARS-CoV-2 reads after CRISPRclean depletion of libraries prepared from contrived samples. CRISPRclean treatment of the fully contrived samples increases the fraction of reads that map to the SARS-CoV-2 genome by an average of ~10-foldResultsCRISPRclean treatment of the contrived samples increases ~10 fold of reads that map to the SARS-CoV-2 genome. For the 60 viral copies of SARS-CoV-2 sample, the number of reads mapping to the SARSCoV-2 genome increases from ~10,000 reads to ~70,000 reads. A similar increase in reads occurs for S. aureus. The percentage of SARS-CoV-2 genome covered at 1X and 10X also increases. Similar results were achieved even after downsampling the datasets to 5M reads. There is a ~4-fold increase in bacterial species detection in these stool samples after CRISPRclean treatment. Percentage of SARS-CoV-2 genome covered at 1X and 10X increases as a result of rRNA depletion. Coverage of the SARS-CoV-2 genome at 50 million reads.Number of reads aligning to the S. aureus and SARS-CoV-2 genomes increases after CRISPRclean depletion. For the sample containing 0.0001% SARS-CoV-2, (60 viral copies), the number of reads mapping to the SARS-CoV-2 genome increases from ~10,000 reads to ~70,000 reads.CosmosID Shotgun Metagenomics Analysis heat map showing read alignments to viral genomes. The yellow color indicates high read counts. The CosmosID shotgun metagenomic analysis software was used to analyze the sequencing data, classify the sequences and generate the heat map.ConclusionMetatranscriptomics powered by CRISPR-mediated rRNA depletion offers a robust methodology to acquire viral genomic data, microbiome composition, co-infection information, and the transcriptional status of the host immune response in a single workflow. This sequencing-based approach can be available on the first day of the next viral outbreak and should be considered as a first-line test for novel zoonotic virus detection. Bacterial species composition of patient stool samples before and after CRISPRclean depletion. ~4-fold increase in bacterial species detection in these stool samples after CRISPRclean treatment. Sequencing data downsampled to 20 million reads.Disclosures Keith Brown, n/a, Jumpcode Genomics (Board Member, Employee, Shareholder)

Development of a DNA Metabarcoding Method for the Identification of Bivalve Species in Seafood Products.

The production of bivalve species has been increasing in the last decades. In spite of strict requirements for species declaration, incorrect labelling of bivalve products has repeatedly been detected. We present a DNA metabarcoding method allowing the identification of bivalve species belonging to the bivalve families Mytilidae (mussels), Pectinidae (scallops), and Ostreidae (oysters) in foodstuffs. The method, developed on Illumina instruments, targets a 150 bp fragment of mitochondrial 16S rDNA. We designed seven primers (three primers for mussel species, two primers for scallop species and a primer pair for oyster species) and combined them in a triplex PCR assay. In each of eleven reference samples, the bivalve species was identified correctly. In ten DNA extract mixtures, not only the main component (97.0–98.0%) but also the minor components (0.5–1.5%) were detected correctly, with only a few exceptions. The DNA metabarcoding method was found to be applicable to complex and processed foodstuffs, allowing the identification of bivalves in, e.g., marinated form, in sauces, in seafood mixes and even in instant noodle seafood. The method is highly suitable for food authentication in routine analysis, in particular in combination with a DNA metabarcoding method for mammalian and poultry species published recently.

Meta-Analysis of Genome-Wide Association Studies of Acute Myeloid Leukemia (AML) Patients Identifies Variants Associated with Risk of 11q23/KMT2A-Translocated and Core-Binding Factor (CBF) AML and Suggests a Role for Transcription Elongation in Leukemogenesis

Meta-Analysis of Genome-Wide Association Studies of Acute Myeloid Leukemia (AML) Patients Identifies Variants Associated with Risk of 11q23/KMT2A-Translocated and Core-Binding Factor (CBF) AML and Suggests a Role for Transcription Elongation in Leukemogenesis

German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing.

We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria. Participants were asked to sequence six DNA samples of three bacterial species (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) in duplicate, according to their routine in-house sequencing protocol. Four different types of Illumina sequencing platforms (MiSeq, NextSeq, iSeq, NovaSeq) and one Ion Torrent sequencing instrument (S5) were involved in the study. Sequence quality parameters were determined for all data sets and centrally compared between laboratories. SNP and cgMLST calling were performed to assess the reproducibility of sequence data collected for individual samples. Overall, we found Illumina short read data to be more accurate (higher base calling accuracy, fewer miss-assemblies) and consistent (little variability between independent sequencing runs within a laboratory) than Ion Torrent sequence data, with little variation between the different Illumina instruments. Two laboratories with Illumina instruments submitted sequence data with lower quality, probably due to the use of a library preparation kit, which shows difficulty in sequencing low GC genome regions. Differences in data quality were more evident after assembling short reads into genome assemblies, with Ion Torrent assemblies featuring a great number of allele differences to Illumina assemblies. Clonality of samples was confirmed through SNP calling, which proved to be a more suitable method for an integrated data analysis of Illumina and Ion Torrent data sets in this study.

Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).

Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5′ end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.

Whole-Exome Sequencing (WES) for Illumina Short Read SequencersUsing Solution-Based Capture.

Next-generation sequencing (NGS) is transforming clinical research and diagnostics, vastly enhancing our ability to identify novel disease-causing genetic mutations and perform comprehensive diagnostic testing in the clinic. Whole-exome sequencing (WES) is a commonly used method which captures the majority of coding regions of the genome for sequencing, as these regions contain the majority of disease-causing mutations. The clinical applications of WES are not limited to diagnosis; the technique can be employed to help determine an optimal therapeutic strategy for a patient considering their mutation profile. WES may also be used to predict a patient's risk of developing a disease, e.g., type 2 diabetes (T2D), and can therefore be used to tailor advice for the patient about lifestyle choices that could mitigate those risks. Thus, genome sequencing strategies, such as WES, underpin the emerging field of personalized medicine. Initiatives also exist for sharing WES data in public repositories, e.g., the Exome Aggregation Consortium (ExAC) database. In time, by mining these valuable data resources, we will acquire a better understanding of the roles of both single rare mutations and specific combinations of common mutations (mutation signatures) in the pathology of complex diseases such as diabetes.Herein, we describe a protocol for performing WES on genomic DNA extracted from blood or saliva. Starting with gDNA extraction, we document preparation of a library for sequencing on Illumina instruments and the enrichment of the protein-coding regions from the library using the Roche NimbleGen SeqCap EZ Exome v3 kit; a solution-based capture method. We include details of how to efficiently purify the products of each step using the AMPure XP System and describe how to use qPCR to test the efficiency of capture, and thus determine finished library quality.

UK regulators get tough on instrument merger

Questions raised by UK regulators recently scuttled one scientific instrument merger and now may lead to trouble for another. The actions anticipate what may be a more active role for UK regulators overseeing international mergers after the UK leaves the European Union. In the most recent instance, the UK’s Competition and Markets Authority (CMA) determined that Illumina’s pending $1.2 billion purchase of DNA-sequencing-systems competitor Pacific Biosciences (PacBio) “could result in more expensive or lower quality products and less innovation in the market.” The CMA threatened to begin an in-depth investigation “if the merging businesses are unable to address the CMA’s concerns.”Both Illumina and PacBio supply instruments that scientists use during disease research and drug development to study genetic variations. Were the two to merge, customers would have “limited alternatives available” for advanced sequencing technology, the CMA says.In December, the CMA questioned another instrumentation deal: Therm...

OR38 Whole gene HLA class I genotyping with the minion nanopore sequencer

In 2014 Oxford Nanopores Technologies released the MinION, a portable miniaturized sequencer delivering multi-kb DNA reads based on nanopore sensing technology. Sequencing accuracy is improved by consecutive sequencing both strands of the DNA (2D reads). Being part of the MinION early access program we evaluated this new technology for whole gene HLA sequencing. As the sequencing yield exceeds the requirements for a targeted approach we developed a strategy for barcoding and demultiplexing of samples. Barcoded amplicons were generated by two subsequent long range PCRs covering the complete genes of HLA-A, -B and -C. Amplicons were pooled and library preparation was performed according to the Oxford Nanopore protocol (SQK-MAP006). Sequencing was performed on a MinION MKI with R7.3 flow cells. NGSengine from GenDX was used for sequence analysis and HLA genotyping. 96 randomly picked class I samples were pooled and sequenced. Over 170,000 reads were generated, approximately 65% of them as 2D reads. Two thirds of the 2D reads could be assigned to a unique barcode sequence. The HLA genotyping results were compared to allelic resolution genotypes obtained by full length sequencing the samples on both Illumina and PacBio instruments. The ONT typing results had a 95% concordance rate when considering 1st to 3rd field. Even when taking the fourth field in account concordance rate was above 90%. Given that the nanopore technology is rapidly evolving and the genotyping software has not yet been optimized for nanopore data, this study clearly underlines the great potential of the MinION for high resolution HLA genotyping.

In Chronic Myeloid Leukemia Patients on 2nd-Line Tyrosine Kinase Inhibitor Therapy, Deep Sequencing at the Time of Warning May Allow Sensitive Detection of Emerging BCR-ABL1 Mutants

▪Background and Aims: Next generation amplicon-based deep sequencing (DS) on the Roche, Illumina or Ion Torrent instruments is becoming accessible to a wider and wider number of diagnostic laboratories. Although conventional sequencing is still the gold standard, DS has been hailed by many as the future of diagnostic BCR-ABL1 kinase domain (KD) mutation screening. BCR-ABL1 KD mutations are infrequent in newly diagnosed chronic myeloid leukemia (CML) patients (pts) receiving 1st-line TKI therapy, but remain a challenge in relapsed pts, who usually display a greater genetic instability. Indeed, pts already harboring BCR-ABL1 KD mutations have a higher likelihood of developing additional, dasatinib (DAS)- or nilotinib (NIL)-resistant mutations – which is defined as a 'failure’ by the 2013 European LeukemiaNet (ELN) recommendations. Taking advantage of a next-generation amplicon sequencing design and protocol set up and validated in the framework of the IRON-II international study, we aimed to assess whether DS may allow a larger window of detection of emerging BCR-ABL1 KD mutants predicting for an impending relapse.Methods: among the imatinib (IM)-resistant CML pts who switched to 2nd-line TKI therapy and were referred to our laboratory for routine BCR-ABL1 transcript level monitoring and KD mutation screening by conventional sequencing, 51 acquired DAS- or NIL-resistant mutations after a median of 9 months (range, 3-27 months) of therapy and had leftover cDNA available at previous timepoints. To reconstruct the dynamics of mutation emergence, resequencing on a Roche GS Junior instrument was performed from the time of failure and mutation detection by conventional sequencing backwards. Runs were designed to achieve high sequencing depth, allowing reliable detection of variants down to 1% abundance. BCR-ABL1/ABL1%IS transcript levels and/or cytogenetic response, whichever available, were used to define whether the patient had an 'optimal response’, 'warning’ or 'failure’ at the time of first mutation detection by DS.Results: baseline mutation status, as assessed by conventional sequencing, was available for all the 51 CML pts included in this retrospective study; 29/51 pts were positive for BCR-ABL1 KD mutations, with switch to NIL or DAS selected accordingly. Twenty-six pts were later found to have acquired DAS-resistant mutations (T315I, n=13; F317L/V, n=10; V299L, n=3) and 25 pts were later found to have acquired NIL-resistant mutations (T315I, n=4; F359V/I/C, n=7; Y253H, n=6; E255K, n=9; one patient acquired two mutations). DS was able to backtrack the DAS- or NIL-resistant mutations to the previous sample(s) in 23/51 (45%) pts. Median mutation burden at the time of first detection by DS was 5% (range, 1-17%); median interval between detection by DS and detection by conventional sequencing was 3 months (range, 3-9 months). In 5 cases, the mutations were traceable at baseline; in the remaining cases, correlation with response at the time mutations were first detected by DS revealed a 'warning’ according to the 2013 ELN definitions of response to 2nd-line therapy in 13 cases; an 'optimal response’ in one case; a 'failure’ in 4 cases. As a control, we used DS to explore BCR-ABL1 KD mutation status in 10 randomly selected pts with 'warning’ at various timepoints, that later turned into optimal responses; no DAS- or NIL-resistant mutations were detected.Conclusions: the 2011 ELN recommendations for mutation analysis suggest BCR-ABL1 KD to be screened by conventional sequencing in case of 'failure’ of 2nd-line TKI therapy – according to the provisional definitions available at the time. Earlier detection of emerging BCR-ABL1 KD mutations allows a greater leeway in tackling drug resistance and enhancing therapeutic efficacy. Data presented herein indicate that:1) DS may reliably pick TKI-resistant mutations earlier than conventional sequencing in a proportion of pts, and that2) the recently introduced definitions of ‘warning’ may provide a rational trigger, besides ‘failure’, for DS-based BCR-ABL1 KD mutation screening in CML pts on 2nd-line TKI therapy.A prospective cost-benefits evaluation of using DS in this and other settings is warranted, and will contribute useful information to the revision of the ELN recommendations for BCR-ABL1 KD mutation analysis.Supported by: European LeukemiaNet, AIL, AIRC, FP7 NGS-PTL project, Progetto Regione-Università 2010-12 (L. Bolondi). DisclosuresSoverini:Novartis: Consultancy; Bristol-Meyers Squibb: Consultancy; Ariad: Consultancy. Castagnetti:Novartis Farma: Consultancy, Honoraria; Bristol Myers Squibb: Consultancy, Honoraria; Pfizer: Consultancy. Gugliotta:Novartis: Consultancy, Honoraria; Bristol Myers Squibb: Consultancy, Honoraria. Bonifacio:Amgen Inc.: Consultancy. Rosti:Novartis: Consultancy; Bristol-Myers Squibb: Consultancy. Baccarani:Novartis: Consultancy; Bristol-Myers Squibb: Consultancy; Ariad: Consultancy; Pfizer: Consultancy. Martinelli:NOVARTIS: Consultancy, Speakers Bureau; BMS: Consultancy, Speakers Bureau; PFIZER: Consultancy; ARIAD: Consultancy.

Comparative Whole Transcriptome Shotgun Sequencing (WTSS) of Myeloma at Diagnosis and at Drug-Resistant Relapse.

Abstract 603 Background:Acquired drug resistance often limits treatment efficacy in multiple myeloma, and may in part be caused by selection for cells bearing mutations conferring drug resistance that were either present in an extant subset of myeloma cells prior to treatment, or were acquired during therapy. We are applying whole transcriptome shotgun sequencing (WTSS) to myeloma BM at diagnosis and drug-resistant relapse, in order to identify gene expression and mutational signatures of drug resistance. We have an archive of frozen myeloma total bone marrow mononuclear cell fractions, as well as a smaller archive of CD138+ enriched specimens. The enriched specimens can be expected to contain purer populations of malignant cells, but may under-represent the heterogeneity of the disease. We are therefore interested in a comparison of the results of WTSS on these two different types of specimens. Methods:Bone marrow from a myeloma patient who responded to front line drug therapy and who subsequently experienced drug resistant disease relapse was identified from our biorepository. RNA was isolated from the total bone marrow mononuclear cell population and from a CD138+ enriched population at diagnosis and at relapse, yielding four samples for analysis (pre-treatment unprocessed, pre-treatment enriched, relapse unprocessed, relapse enriched). Poly-adenylated RNA from each of the four samples was converted to cDNA using a random primed approach, and paired-end sequences collected using Illumina instruments. Results:We sequenced the transcriptomes of the four samples by generating a total of 694,076,590 36- and 50-mer sequences (30,681,959,896 base-pairs). Of these, 325,998,000 (14,063,396,516 base-pairs) were mapped to reference genome or transcriptome databases using MAQ. Each base in 3,094 transcripts was represented at a minimum of 6 fold redundant coverage. 68.57 % (223,555,599) of the reads matched perfectly to reference sequences. Reads containing single nucleotide mismatches to the reference sequence were evaluated using a Bayesian mixture model to estimate the presence of single nucleotide variants (SNVs) which yielded 89,944 high confidence predictions divided amongst the four samples. Of these, 74,704 (83.1%) were identical to known SNVs present in dbSNP and other sequence datasets, and 13,073 represented non-coding or synonymous variants. The remaining 2,167 mismatches most likely represent undiscovered variants also present in the patient's normal DNA or somatic mutations. These two possibilities will be distinguished by sequencing the candidate variants using DNA purified from the patient's non-malignant cells. For candidate sequence variant positions well represented at the position and gene level in each of the two sample pairs we were comparing (pre- and post-treatment unprocessed, and pre- and post-treatment enriched) we found 85 unique to the pre-treatment enriched sample, 145 unique to the post-treatment enriched sample, 250 unique to the pre-treatment unprocessed sample and 51 unique tunique o the post-treatment unprocessed sample. Some of the genes affected by these candidate mutations include genes that have previously been observed in cancer, such as PIM2, SHC1 and SCRIB. Gene expression levels were estimated using the previously published RPKM (reads per kilobase of exon model per million mapped reads) metric. For the unprocessed samples, 108 genes were found to be up-regulated pre-treatment and 95 post-treatment. The enriched samples presented 80 genes with higher expression before treatment and 54 after treatment. Because we are using a paired end sequencing approach, the potential exists to identify candidate expressed gene fusions. Initial searches for candidate gene fusion events have resulted in the detection of a fusion involving IgH and MMSET, corresponding to a t(4;14) translocation which had previously been detected with standard methods. Discussion:It is possible to sequence and compare the expressed myeloma genome of patients at diagnosis and at relapse with WTSS, in order to gain insight into the evolution of myeloma under drug selection and its role in the development of treatment resistance. With the study of a larger cohort of patients and subsequent functional characterization of the candidate sequence variants, we hope to identify recurrent mechanisms of myeloma drug resistance which might be amenable to therapeutic intervention. Disclosures:No relevant conflicts of interest to declare.