ALBERT

Description: Bone marrow failure syndromes (BMFS) are a diverse group of rare life-threatening blood disorders characterized by inadequate hematopoiesis, clonal evolution, and increased risk of hematologic malignancies. Despite recent advances in the understanding of the molecular pathogenesis of BMFS, the ability to diagnose, risk-stratify, and treat patients with these rare disorders remains limited. In both the acquired and the inherited BMFS, the major contributors to mortality are complications of progressive cytopenias, and, albeit to a lesser extent—transformation to myelodysplastic syndrome (MDS) and acute myeloid leukemia. The main predictor of malignant transformation is acquisition of clonal cytogenetic abnormalities. Recently, single nucleotide polymorphism arrays (SNP-A) were proposed as a promising tool for high resolution cytogenetic analysis and surveillance of early clonal changes in BMFS, however, their clinical utility still remains to be established. In 2009, the Comprehensive Bone Marrow Failure Center at the Children’s Hospital of Philadelphia and the Hospital of the University of Pennsylvania incorporated high-density SNP-A as an adjunct to conventional cytogenetics in evaluation of BMFS patients. Here we present a comprehensive analysis of genetic changes in BMFS using 124 SNP-A from 91 patients, who were referred for evaluation of bone marrow failure. SNP-A genotyping was correlated with medical histories, hematopathology, cytogenetic, and molecular data. To assess the potential role of SNP-A in screening for early clonal evolution, longitudinal analysis of SNP-A was performed in 25 patients. We found that acquired copy number-neutral loss of heterozygosity (CN-LOH) was significantly more frequent in acquired aplastic anemia (aAA) than in other BMFS (OR 12.240, 95% CI 1.333-573.696, p

Description: Acquired aplastic anemia (AA) is a rare bone marrow failure syndrome. AA is believed to be immune-mediated, supported by in vitro studies and the success of empiric immunosuppressive therapy. Recently, a chromosomal alteration-copy number-neutral loss of heterozygosity of chromosome arm 6p, the site of the Major Histocompatibility Complex and the Human Leukocyte Antigen (HLA) genes-has been identified as a recurrent somatic change in AA. Clonal hematopoiesis marked by 6p CN-LOH is hypothesized to emerge by immune escape of hematopoietic cells lacking certain HLA alleles. However, because of the large size of the genomic region involved by 6p CN-LOH and the strong linkage disequilibrium among other genes in the region, specific alleles targeted by the immune selection in AA are unknown. In a previous study, we reported two patients with somatic loss-of-function mutations in HLA class I genes, leading us to hypothesize that loss of HLA alleles in AA may be common and likely defines a subset of patients with unique characteristics and disease course. To characterize the prevalence of HLA allele loss in AA, we performed targeted next generation sequencing of HLA-A, B, and C genes, in conjunction with single nucleotide polymorphism array genotyping of bone marrow (BM) or peripheral blood DNA in 74 patients with AA. 52 patients had pediatric-onset AA, and 22 had adult-onset AA. Somatic status of mutations was confirmed by sequencing paired constitutional DNA. Eleven patients (15%) were found to have somatic loss of HLA alleles: 5 patients had 6p CN-LOH, 3 patients had loss-of-function mutations (frameshift, nonsense, or start codon loss) of the HLA class I alleles, and 3 patients were found to have both 6p CN-LOH as well as loss-of-function HLA mutations. HLA loss was more frequent in pediatric-onset AA (9 of 52 patients, 17%) as compared to adults (2 of 22 patients, 9%), although the difference did not reach statistical significance. No HLA mutations were identified in 19 patients with classical Paroxysmal Nocturnal Hemoglobinuria, nor in 20 healthy relatives (p=0.06). Among the 11 patients with somatic HLA loss, 8 patients had evidence of oligoclonal hematopoiesis with several independent clones carrying different alterations of the same HLA allele. Among the 6 patients with loss-of-of function HLA mutations, the median number of HLA mutations per patient was 1.5 (range 1-3). Of the 8 patients with acquired 6p CN-LOH, the median number of distinct 6p CN-LOH events per patient was 2 (range 1-4). In the 3 patients harboring both 6p CN-LOH as well as the loss-of-function HLA mutations, both mechanisms led to the recurrent loss of the same allele. Strikingly, only a few distinct HLA class I alleles were targeted by mutations. The most frequently affected were HLA-B*40:02:01 (5 independent mutations in 2 patients) and HLA-B*14:02:01 (3 mutations in 2 patients, and as well as loss through polyclonal 6p CN-LOH in 2 patients). Additionally, one patient each had loss of HLA-A*68:01:01 and HLA-A*33:03:01 through mutational inactivation as well as through 6p CN-LOH. To investigate whether HLA mutations are sufficient to cause clonal expansion or whether other somatic mutations are required, we performed comparative whole exome sequencing (WES) of paired BM and skin DNA in five patients carrying inactivating HLA mutations. Four of the five patients had no other mutations affecting protein sequence or untranslated regulatory regions. One patient had additional somatic mutations, which were subclonal to and co-segregated with the three independent inactivating mutations in the HLA-B*40:02:01 allele. Serial follow-up confirmed that HLA mutations persisted overtime, with a relative expansion of one of the HLA-B*40:02:01 mutant clones bearing a protein-altering mutation in the BCL9 gene. Our results show that loss of HLA class I alleles is common in AA, second only to PIGA gene mutations. The affected alleles are non-random, with immune selection most commonly targeting HLA-B* 40:02:01 and HLA-B*14:02:01 alleles, providing the first evidence of specificity of immune attack in AA. The resultant hematopoiesis caused by selection of cells with HLA allele loss is typically oligoclonal and commonly occurs in the absence of other somatic mutations. Acquisition of additional mutations can lead to clonal dominance overtime. Further studies are underway to better understand the role of HLA loss in patient outcomes and AA pathogenesis. Disclosures No relevant conflicts of interest to declare.

Description: Background Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. Results We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. Conclusions To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects. Availability and Implementation Available on the web at: http://sourceforge.net/projects/cnv

Description: Background Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and/or the Illumina Genome Analyzer II next generation sequencing platform. Results An average call rate of 99.75% was achieved across all samples with our custom pipeline. Comparison of calls for 15 samples characterized previously by Sanger sequencing revealed a total of 29 discordant calls, which translates to an estimated 0.012% for the base call error rate. We successfully identified 4 known heteroplasmic mutations and 24 other potential heteroplasmic mutations across 20 samples that passed quality control. Conclusions Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis.