An open-source python library for detection of known and novel Kell, Duffy and Kidd variants from exome sequencing

BACKGROUND AND OBJECTIVES

Next generation sequencing (NGS) has promising applications in transfusion medicine. Exome sequencing (ES) is increasingly used in the clinical setting, and blood group interpretation is an additional value that could be extracted from existing data sets. We provide the first release of an open-source software tailored for this purpose and describe its validation with three blood group systems.

MATERIALS AND METHODS

The DTM-Tools algorithm was designed and used to analyse 1018 ES NGS files from the ClinSeq® cohort. Predictions were correlated with serology for 5 antigens in a subset of 108 blood samples. Discrepancies were investigated with alternative phenotyping and genotyping methods, including a long-read NGS platform.

RESULTS

Of 116 genomic variants queried, those corresponding to 18 known KEL, FY and JK alleles were identified in this cohort. 596 additional exonic variants were identified KEL, ACKR1 and SLC14A1, including 58 predicted frameshifts. Software predictions were validated by serology in 108 participants; one case in the FY blood group and three cases in the JK blood group were discrepant. Investigation revealed that these discrepancies resulted from (1) clerical error, (2) serologic failure to detect weak antigenic expression and (3) a frameshift variant absent in blood group databases.

CONCLUSION

DTM-Tools can be employed for rapid Kell, Duffy and Kidd blood group antigen prediction from existing ES data sets; for discrepancies detected in the validation data set, software predictions proved accurate. DTM-Tools is open-source and in continuous development.

A multi-dimensional analysis of genotype-phenotype discordance in malignant hyperthermia susceptibility

BACKGROUND

Malignant hyperthermia (MH) susceptibility is an inherited condition, diagnosed either by the presence of a pathogenic genetic variant or by in vitro caffeine-halothane contracture testing. Through a multi-dimensional approach, we describe the implications of discordance between genetic and in vitro test results in a patient with a family history of possible MH.

METHODS

The patient, whose brother had a possible MH reaction, underwent the caffeine-halothane contracture test (CHCT) according to the North American MH Group protocol. Screening of the complete RYR1 and CACNA1S transcripts was done using Sanger sequencing. Additional functional analyses included skinned myofibre calcium-induced calcium release sensitivity, calcium signalling assays in cultured myotubes, and in silico evaluation of the effect of any genetic variants on their chemical environment.

RESULTS

The patient's CHCT result was negative but she carried an RYR1 variant c.1209C>G, p.Ile403Met, that is listed as pathogenic by the European Malignant Hyperthermia Group. Functional tests indicated a gain-of-function effect with a weak impact, and the variant was predicted to affect the folding stability of the 3D structure of the RyR1 protein. Based on American College of Medical Genetics and Genomics/Association of Molecular Pathology guidelines, this variant would be characterised as a variant of uncertain significance.

CONCLUSIONS

Available data do not confirm or exclude an increased risk of MH for this patient. Further research is needed to correlate RyR1 functional assays, including the current gold standard testing for MH susceptibility, with clinical phenotypes. The pathogenicity of genetic variants associated with MH susceptibility should be re-evaluated.

OR11-6 Rare Sequence Variants in GnRH-Associated Genes May Contribute to Variable Susceptibility to Environmental Stressors in Functional Hypothalamic Amenorrhea

Some, but not all, women develop hypothalamic amenorrhea (HA) in association with exercise and/or food restriction. We hypothesized that variants in genes associated with the more severe hypogonadotropic disorder, idiopathic hypogonadotropic hypogonadism (IHH), may contribute to a given woman’s susceptibility to HA when she is faced with a physiologic stressor. Indeed, rare sequence variants (RSVs) in IHH-associated genes were previously identified in women with HA that were absent in controls¹. This study, however, used a variant-level, as opposed to the now preferred gene-level, approach and only examined 7 genes. To build upon these earlier findings and provide more definitive support for our hypothesis, we screened 106 women with HA and 477 controls for RSVs in a much larger IHH-gene panel (n=54 genes) using exome sequencing. Healthy controls were a convenience sample drawn from the ClinSeq Project² who had originally been selected for a range of atherosclerosis risk phenotypes, but were unselected for reproductive phenotypes. We compared the frequency of RSVs (moderate- to high-impact, minor allele frequency [MAF] < 1%) across all 54 genes in HA compared with controls using a rare variant burden test (Fisher’s exact test. We identified 54 heterozygous RSVs (51 missense, 1 nonsense, 2 frameshift; 27.4% of alleles) in 46 HA women (1-3 RSVs/woman, 58 total RSVs, 12 subjects with >1 RSV) and 149 heterozygous RSVs (141 missense, 1 nonsense, 4 frameshift, 3 inframe indels; 18.8%) in 146 control women (1-4 RSVs/woman, 179 total RSVs, 28 subjects with >1 RSV) which represents a significantly increased burden of RSVs in HA (P = 0.006). A slightly greater proportion of RSVs in the HA group were considered damaging/deleterious by both Polyphen2 and SIFT vs controls (41.1% vs 36.0%), but this was not statistically significant. Thus, women with HA are significantly enriched for RSVs in genes that cause IHH as compared with controls. These results indicate that the risk of developing HA with exposure to physiologic stressors may indeed be increased in the presence of heterozygous protein-altering variants in genes related to the regulation of GnRH neuronal development and function. ¹ Caronia LM, et al. N Engl J Med. 2011;364:215-25. ² Biesecker LG, et al. Genome Res. 2009;19:1665-74. Unless otherwise noted, all abstracts presented at ENDO are embargoed until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. Abstracts presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.

Determining the prevalence of McArdle disease from gene frequency by analysis of next-generation sequencing data

Purpose

McArdle disease is one of the most common glycogen storage disorders. Although the exact prevalence is not known, it has been estimated to be 1 in 100,000 patients in the United States. More than 100 mutations in PYGM have been associated with this disorder. McArdle disease has significant clinical variability with some patients presenting with severe muscle pain and weakness while others have only mild, exercise-related symptoms.

Methods

Next-Generation sequencing data allow estimation of disease prevalence with minimal ascertainment bias. We analyzed gene frequencies in two cohorts of patients from exome sequencing results. We categorized variants into three groups: a curated set of published mutations, variants of uncertain significance, and likely benign variants.

Results

An initial estimate based on the frequency of six common mutations predicts a disease prevalence of 1/7,650 (95% CI 1/5,362 to 1/11,108), which greatly deviates from published estimates. A second method using the two most common mutations predicts a prevalence of 1/42,355 (95% CI 1/24,536 - 1/76,310) in Caucasians.

Conclusions

These results suggest that the currently accepted prevalence of McArdle disease is an underestimate and that some of the currently considered pathogenic variants are likely benign.

TREML4 expression by myeloid cells may play a role in coronary artery disease (HUM1P.308)

Triggering Receptor Expressed on Myeloid cells (TREM) family receptors modulate responses of a variety of leukocytes. We found that TREM-like 4 (TREML4) mRNA is elevated in the peripheral blood of patients with advanced coronary artery calcification (CAC) and that a single nucleotide polymorphism (SNP), rs2803496, tracks with the level of TREML4 mRNA in these patients. In an effort to elucidate the mechanism through which TREML4 in peripheral blood could affect CAC, we began by determining what cells express it. Monocytes and lymphocytes of donors with this SNP expressed very low levels of TREML4 mRNA whereas their neutrophils (PMNs) were strongly positive. Consistent with its association with CAC, we found variation in the levels of TREML4 mRNA in PMNs that correlated rs2803496, and a second SNP rs2803495. Unlike murine Treml4, which has the typical TREM family structure, human TREML4 has a noncanonical leader, lacks a portion of the transmembrane domain (TM) and has no cytoplasmic tail. Characterization of the Treml4 cDNA suggests that this truncated TM domain is sufficient to anchor the protein in the plasma membrane but that the TREML4 native leader sequence is ineffective. Lastly, immunostaining of human atherosclerotic plaques shows TREML4 in macrophage-rich regions, as well as on the endothelium. Together our findings suggest that TREML4 may play an important role in atherosclerosis and CAC but that it is unlikely to function as a typical, DAP12-coupled TREM.

Improving the rigor of mutation reports: biologic parentage and de novo mutations

The accurate determination and dissemination of the causality or pathogenicity of human DNA sequence variants is a crucial function of genetics journals. Published reports of pathogenic mutations are a common source of information for mutation databases, which are in turn used to make recommendations to patients. One of the strongest pieces of evidence in support of causality or pathogenicity for mutation reports is the occurrence of a de novo mutation. Yet, many publications describing such changes do not demonstrate that the mutation is truly de novo, by performing biologic parentage testing. I argue here that all mutation reports that describe such mutations should include biologic parentage testing, or in the absence of such testing, the mutation should be described as "apparently de novo." This proposed standard should improve the transparency of the evidence that underlies our literature, and ultimately improve the databases of mutations in human disease.

A recurrent loss-of-function alanyl-tRNA synthetase (AARS) mutation in patients with Charcot-Marie-Tooth disease type 2N (CMT2N)

Charcot-Marie-Tooth (CMT) disease comprises a heterogeneous group of peripheral neuropathies characterized by muscle weakness and wasting, and impaired sensation in the extremities. Four genes encoding an aminoacyl-tRNA synthetase (ARS) have been implicated in CMT disease. ARSs are ubiquitously expressed, essential enzymes that ligate amino acids to cognate tRNA molecules. Recently, a p.Arg329His variant in the alanyl-tRNA synthetase (AARS) gene was found to segregate with dominant axonal CMT type 2N (CMT2N) in two French families; however, the functional consequence of this mutation has not been determined. To investigate the role of AARS in CMT, we performed a mutation screen of the AARS gene in patients with peripheral neuropathy. Our results showed that p.Arg329His AARS also segregated with CMT disease in a large Australian family. Aminoacylation and yeast viability assays showed that p.Arg329His AARS severely reduces enzyme activity. Genotyping analysis indicated that this mutation arose on three distinct haplotypes, and the results of bisulfite sequencing suggested that methylation-mediated deamination of a CpG dinucleotide gives rise to the recurrent p.Arg329His AARS mutation. Together, our data suggest that impaired tRNA charging plays a role in the molecular pathology of CMT2N, and that patients with CMT should be directly tested for the p.Arg329His AARS mutation.

Parenting children with Proteus syndrome: experiences with, and adaptation to, courtesy stigma

Courtesy stigma refers to the stigmatization an unaffected person experiences due to his or her relationship with a person who bears a stigma. Parents of children with genetic conditions are particularly vulnerable to courtesy stigma, but little research has been done to explore this phenomenon. The purpose of this study was to investigate the courtesy stigma experiences of parents of children with Proteus syndrome (PS) and related overgrowth conditions. Thematic analysis of transcripts from 31 parents identified three distinct themes: stigma experiences, social-emotional reactions to stigmatizing encounters, and coping responses. Four types of stigmatizing experiences were identified: intrusive inquires, staring and pointing, devaluing remarks, and social withdrawal. Additionally, we uncovered eight strategies parents used to cope with courtesy stigma: attributing cause, assigning meaning to social exchanges, concealing, withdrawing socially, taking the offensive, employing indifference, instructing and learning from family, and educating others. Parents' choices of strategy type were found to be context dependent and evolved over time. This is the first study to document the adaptive evolution of coping strategies to offset courtesy stigma by parents of children with genetic conditions. These results provide groundwork for genetic counseling interventions aimed at addressing issues of courtesy stigma and further investigation of the phenomenon itself.

The challenges of Proteus syndrome: diagnosis and management

Proteus syndrome (PS) is a disorder of patchy or mosaic postnatal overgrowth of unknown etiology. The onset of overgrowth typically occurs in infancy and can involve any tissue of the body. Commonly involved tissues include connective tissue and bone, skin, central nervous system, the eye, but it apparently can affect any tissue. Diagnosing of PS is difficult and the diagnostic criteria are controversial. Our group advocates stringent diagnostic criteria to facilitate research and appropriate clinical care. The benefit of strict criteria is that they define a clinical group that is reasonably homogenous with respect to manifestations and prognosis. The overgrowth of PS is progressive and can be difficult to manage. The progressive overgrowth most commonly causes severe orthopaedic complications, but it can cause many other complications. One of the most common complications in patients with PS is deep venous thrombosis and pulmonary embolism, which can cause premature death. Effective management requires knowledge of the wide array of manifestations and complications of the disorder and a team approach that includes the geneticist, surgeons, and other specialists.

Screening for submicroscopic chromosome rearrangements in children with idiopathic mental retardation using microsatellite markers for the chromosome telomeres

Recently much attention has been given to the detection of submicroscopic chromosome rearrangements in patients with idiopathic mental retardation. We have screened 27 subjects with mental retardation and dysmorphic features for such rearrangements using a genetic marker panel screening. The screening was a pilot project using markers from the subtelomeric regions of all 41 chromosome arms. The markers were informative for monosomy in both parents at 3661902 loci (40.6%, 95% confidence interval 37.0-44.2%) in the 22 families where DNA was available from both parents. In two of the 27 subjects, submicroscopic chromosomal aberrations were detected. The first patient had a 5-6 Mb deletion of chromosome 18q and the second patient had a 4 Mb deletion of chromosome 1p. The identification of two deletions in 27 cases gave an aberration frequency of 7.5% without adjustment for marker informativeness (95% confidence interval 1-24%) and an estimated frequency of 18% if marker informativeness for monosomy was taken into account. This frequency is higher than previous estimates of the number of subtelomeric chromosome abnormalities in children with idiopathic mental retardation (5-10%) although the confidence interval is overlapping. Our study suggests that in spite of the low informativeness of this pilot screening, submicroscopic chromosome aberrations may be a common cause of dysmorphic features and mental retardation.

Diverse mutations in the gene for cartilage oligomeric matrix protein in the pseudoachondroplasia-multiple epiphyseal dysplasia disease spectrum

Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are autosomal dominant osteochondrodysplasias that result in mild to severe short-limb dwarfism and early-onset osteoarthrosis. PSACH and some forms of MED result from mutations in the gene for cartilage oligomeric matrix protein (COMP; OMIM 600310 [http://www3.ncbi.nlm. nih.gov:80/htbin-post/Omim/dispmim?600310]). We report the identification of COMP mutations in an additional 14 families with PSACH or MED phenotypes. Mutations predicted to result in single-amino acid deletions or substitutions, all in the region of the COMP gene encoding the calmodulin-like repeat elements, were identified in patients with moderate to severe PSACH. We also identified within this domain a missense mutation that produced MED Fairbank. In two families, one with mild PSACH and the second with a form of MED, we identified different substitutions for a residue in the carboxyl-terminal globular region of COMP. Both the clinical presentations of these two families and the identification of COMP-gene mutations provide evidence of phenotypic overlap between PSACH and MED. These data also reveal a role for the carboxyl-terminal domain in the structure and/or function of COMP.

Spectral karyotyping refines cytogenetic diagnostics of constitutional chromosomal abnormalities

Karyotype analysis by chromosome banding is the standard method for identifying numerical and structural chromosomal aberrations in pre- and postnatal cytogenetics laboratories. However, the chromosomal origins of markers, subtle translocations, or complex chromosomal rearrangements are often difficult to identify with certainty. We have developed a novel karyotyping technique, termed spectral karyotyping (SKY), which is based on the simultaneous hybridization of 24 chromosome-specific painting probes labeled with different fluorochromes or fluorochrome combinations. The measurement of defined emission spectra by means of interferometer-based spectral imaging allows for the definitive discernment of all human chromosomes in different colors. Here, we report the comprehensive karyotype analysis of 16 samples from different cytogenetic laboratories by merging conventional cytogenetic methodology and spectral karyotyping. This approach could become a powerful tool for the cytogeneticists, because it results in a considerable improvement of karyotype analysis by identifying chromosomal aberrations not previously detected by G-banding alone. Advantages, limitations, and future directions of spectral karyotyping are discussed.

Characterization of familial partial 10p trisomy by chromosomal microdissection, FISH, and microsatellite dosage analysis

Unbalanced translocations are a frequent cause of multiple congenital anomalies in children. Translocations as small as 2-5 Mb of DNA are detectable by G-banding under optimal conditions. Some of these small translocations are visible but cannot be characterized cytogenetically due to the lack of characteristic banding on Giemsa preparations. We have combined chromosomal microdissection and fluorescence in situ hybridization (FISH) to identify the origin of a small translocated segment in three members of a family with a derivative chromosome 9 and multiple anomalies, including several ophthalmologic anomalies. We microdissected the abnormal region of the derivative 9 chromosome and used this DNA to generate a FISH probe. This probe hybridized to distal 10p on the metaphase spread of the proband, indicating the origin of the translocated segment. A whole 10p FISH probe confirmed the origin by hybridizing to the translocated segment of the derivative chromosome. FISH was then performed with a whole chromosome 9 painting probe and excluded the presence of a reciprocal, balancing translocation. We then studied the chromosome 10 partial duplication with microsatellite markers to better characterize the chromosomal segment that caused these phenotypic features. By examining the involved areas with distal 10p and 9p microsatellite markers, we were able to demonstrate a minimum of 9 Mb of trisomic 10p DNA with a chromosomal breakpoint between 10p14-10p15. We then compared this family's clinical findings to those of individuals with partial 10p trisomy who had been reported in the literature. The clinical phenotypes seen in this family are similar to, but milder than, the phenotypes of persons with the larger partial trisomies of 10p that were diagnosable by cytogenetic analysis alone. This study shows that microdissection and DNA markers can be used to precisely define small translocations that are difficult to identify by conventional G-banded chromosome analysis.