David Dimmock

Guidelines for investigating causality of sequence variants in human disease

The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

Purpose: We report a male child who presented at 15 months with perianal abscesses and proctitis, progressing to transmural pancolitis with colocutaneous fistulae, consistent with a Crohn disease-like illness. The age and severity of the presentation suggested an underlying immune defect; however, despite comprehensive clinical evaluation, we were unable to arrive at a definitive diagnosis, thereby restricting clinical management.Methods: We sought to identify the causative mutation(s) through exome sequencing to provide the necessary additional information required for clinical management.Results: After sequencing, we identified 16,124 variants. Subsequent analysis identified a novel, hemizygous missense mutation in the X-linked inhibitor of apoptosis gene, substituting a tyrosine for a highly conserved and functionally important cysteine. X-linked inhibitor of apoptosis was not previously associated with Crohn disease but has a central role in the proinflammatory response and bacterial sensing through the NOD signaling pathway. The mutation was confirmed by Sanger sequencing in a licensed clinical laboratory. Functional assays demonstrated an increased susceptibility to activation-induced cell death and defective responsiveness to NOD2 ligands, consistent with loss of normal X-linked inhibitor of apoptosis protein function in apoptosis and NOD2 signaling.Conclusions: Based on this medical history, genetic and functional data, the child was diagnosed as having an X-linked inhibitor of apoptosis deficiency. Based on this finding, an allogeneic hematopoietic progenitor cell transplant was performed to prevent the development of life-threatening hemophagocytic lymphohistiocytosis, in concordance with the recommended treatment for X-linked inhibitor of apoptosis deficiency. At >42 days posttransplant, the child was able to eat and drink, and there has been no recurrence of gastrointestinal disease, suggesting this mutation also drove the gastrointestinal disease. This report describes the identification of a novel cause of inflammatory bowel disease. Equally importantly, it demonstrates the power of exome sequencing to render a molecular diagnosis in an individual patient in the setting of a novel disease, after all standard diagnoses were exhausted, and illustrates how this technology can be used in a clinical setting.

Assuring the quality of next-generation sequencing in clinical laboratory practice

Amy S Gargis, Centers for Disease Control and Prevention Lisa Kalman, Centers for Disease Control and Prevention Meredith W Berry, SeqWright Inc David P Bick, Medical College of Wisconsin David P Dimmock, Medical College of Wisconsin Tina Hambuch, Illumina Clinical Services Fei Lu, SeqWright Inc Elaine Lyon, University of Utah Karl V Voelkerding, University of Utah Barbara Zehnbauer, Emory University

Exploring concordance and discordance for return of incidental findings from clinical sequencing

Purpose:The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.Methods:Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic.Results:On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.Conclusion:Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405–410

Successful immune tolerance induction to enzyme replacement therapy in CRIM-negative infantile Pompe disease

Purpose:Infantile Pompe disease resulting from a deficiency of lysosomal acid α-glucosidase (GAA) requires enzyme replacement therapy (ERT) with recombinant human GAA (rhGAA). Cross-reactive immunologic material negative (CRIM-negative) Pompe patients develop high-titer antibody to the rhGAA and do poorly. We describe successful tolerance induction in CRIM-negative patients.Methods:Two CRIM-negative patients with preexisting anti-GAA antibodies were treated therapeutically with rituximab, methotrexate, and gammaglobulins. Two additional CRIM-negative patients were treated prophylactically with a short course of rituximab and methotrexate, in parallel with initiating rhGAA.Results:In both patients treated therapeutically, anti-rhGAA was eliminated after 3 and 19 months. All four patients are immune tolerant to rhGAA, off immune therapy, showing B-cell recovery while continuing to receive ERT at ages 36 and 56 months (therapeutic) and 18 and 35 months (prophylactic). All patients show clinical response to ERT, in stark contrast to the rapid deterioration of their nontolerized CRIM-negative counterparts.Conclusion:The combination of rituximab with methotrexate ± intravenous gammaglobulins (IVIG) is an option for tolerance induction of CRIM-negative Pompe to ERT when instituted in the naïve setting or following antibody development. It should be considered in other conditions in which antibody response to the therapeutic protein elicits robust antibody response that interferes with product efficacy.Genet Med 2012:14(1):135–142

Whole exome and whole genome sequencing.

Purpose of review The purpose of this review is to describe the new DNA sequencing technologies referred to as next-generation sequencing (NGS). These new methods are becoming central to research in human disease and are starting to be used in routine clinical care. Recent findings Advances in instrumentation have dramatically reduced the cost of DNA sequencing. An individuals entire genome can now be sequenced for

Clinical and molecular features of mitochondrial DNA depletion due to mutations in deoxyguanosine kinase.

7500. In addition, the software needed to analyze and help interpret this data is rapidly improving. This technology has been used by researchers to discover new genetic disorders and new disease associations. In the clinic, it can define the etiology in patients with undiagnosed genetic disorders and identify mutations in a cancer to help guide chemotherapy. Summary Here we discuss how whole-exome sequencing and whole-genome sequencing are used in basic research and clinical care. These new techniques promise to speed research and affect how healthcare is delivered.

Quantitative Evaluation of the Mitochondrial DNA Depletion Syndrome

Published mutations in deoxyguanosine kinase (DGUOK) cause mitochondrial DNA depletion and a clinical phenotype that consists of neonatal liver failure, nystagmus and hypotonia. In this series, we have identified 15 different mutations in the DGUOK gene from 9 kindreds. Among them, 12 have not previously been reported. Nonsense, splice site, or frame‐shift mutations that produce truncated proteins predominate over missense mutations. All patients who harbor null mutations had early onset liver failure and significant neurological disease. These patients have all died before 2‐years of age. Conversely, two patients carrying missense mutations had isolated liver disease and are alive in their 4th year of life without liver transplant. Five subjects were detected by newborn screening, with elevated tyrosine or phenylalanine. Consequently, this disease should be considered if elevated tyrosine is identified by newborn screening. Mitochondrial DNA content was below 10% of controls in liver in all but one case and modestly reduced in blood cells. With this paper a total of 39 different mutations in DGUOK have been identified. The most frequent mutation, c.763_c.766dupGATT, occurs in 8 unrelated kindreds. 70% of mutations occur in only one kindred, suggesting full sequencing of this gene is required for diagnosis. The presentation of one case with apparent viral hepatitis, without neurological disease, suggests that this disease should be considered in patients with infantile liver failure regardless of the presence of neurological features or apparent infectious etiology.

A timely arrival for genomic medicine

BACKGROUND The mitochondrial DNA (mtDNA) depletion syndromes (MDDSs) are autosomal recessive disorders characterized by a reduction in cellular mtDNA content. Mutations in at least 9 genes [POLG, polymerase (DNA directed), gamma; DGUOK, deoxyguanosine kinase; TK2, thymidine kinase, mitochondrial; TYMP, thymidine phosphorylase; MPV17, MpV17 mitochondrial inner membrane protein; SUCLA2, succinate-CoA ligase, ADP-forming, beta subunit; SUCLG1, succinate-CoA ligase, alpha subunit; RRM2B, RRM2B, ribonucleotide reductase M2 B (TP53 inducible); and C10orf2, chromosome 10 open reading frame 2 (also known as TWINKLE)] have been reported to cause mtDNA depletion. In the clinical setting, a simple method to quantify mtDNA depletion would be useful before undertaking gene sequence analysis. METHODS Real-time quantitative PCR (qPCR) was used to measure the mtDNA content in blood, muscle, and liver samples and in skin fibroblast cultures from individuals suspected of mitochondrial disorders, with or without deleterious mutations in genes responsible for MDDS. RESULTS The mtDNA content was quantified in 776 tissue samples (blood, n = 341; muscle, n = 325; liver, n = 63; skin fibroblasts, n = 47) from control individuals. mtDNA content increased with age in muscle tissue, decreased with age in blood samples, and appeared to be unaffected by age in liver samples. In 165 samples (blood, n = 122; muscle, n = 21; liver, n = 15; skin fibroblasts, n = 7) from patients with molecularly proven MDDSs, severe mtDNA depletion was detected in liver and muscle tissue with high specificity and sensitivity. Blood samples were specific but not sensitive for detecting mtDNA depletion, and skin fibroblasts were not valuable for evaluating mtDNA depletion. Mutations in the POLG, RRM2B, and MPV17 genes were prospectively identified in 1 blood, 1 liver, and 3 muscle samples. CONCLUSIONS Muscle and liver tissues, but not blood or skin fibroblasts, are potentially useful for rapid screening for mtDNA depletion with real-time qPCR.

Allogeneic hematopoietic cell transplantation for XIAP deficiency: an international survey reveals poor outcomes

In this issue of GIM,1 we describe a young boy who presented with unusually aggressive inflammatory bowel disease refractory to medical and surgical treatment. To reach a diagnosis, we were compelled to use genomic technology that, at the time, was not a clinically validated test. This case stimulated many discussions within our group and institution on the boundary between research and clinical care. Many of the same issues were raised again during review of the manuscript, further shaping our thinking about how this case speaks to the broader issue of genomics in medical practice. The purpose of this commentary is to expound on these issues, hopefully to stimulate discussion within the wider medical community. CLINICAL COURSE AND THE DECISION TO SEQUENCE Our article1 provides an abbreviated history of this patient’s unusual clinical course. In this limited space, it is difficult to convey the profound disability and suffering the child endured through numerous long hospital stays, and the resulting frustration that we experienced as we struggled to control the disease. Over a 3-year period, there were more than 100 surgical procedures, clinical consultations with physicians from around the world, innumerable informal discussions, weekly clinical care meetings, and informal e-mail consultations with world-leading experts. Despite these measures, we enjoyed little strategic success. Allogeneic hematopoietic progenitor cell transplant was regularly brought up as a potential therapy, but two main barriers prevented us from moving forward. First, for the majority of the clinical course, the child was judged to be too ill to have a reasonable chance of surviving the first 100 days of the transplant process. Second, we lacked a firm diagnosis; hence, we could not predict whether bone marrow transplant would be likely to help. However, the risks of morbidity and mortality were high. Although the disease could be intermittently brought into remission, it was felt that eventually the child would succumb to drug toxicity, total parenteral nutrition liver disease, or recurrence. Thus, from a therapeutic standpoint, we were left with no viable long-term options. The disease shared some similarities with Crohn disease, but the severity and tempo of disease progression was highly atypical. Exhaustive efforts to reach a diagnosis revealed numerous abnormalities in this child’s immune system, but none of these were pathognomonic for a specific disease. Similarly, conventional genetic testing of numerous candidate genes had failed to reach an answer. Therefore, we decided the next logical step was to sequence the patient’s exome (all known exons within the patient’s genome). FROM DATA TO DIAGNOSIS Initially, we formulated the following hypothesis: the disease was likely to be a single gene disorder with a recessive mode of inheritance. As we were looking for a recessive disease with a population frequency of 1:10,000, we could exclude genetic variants found in more than 1% of the general population as being causal of the child’s disease. Initial analysis was limited to a set of 2006 target genes to reduce the risk of discovering off target information. After it was clear that none of the candidate genes harbored a pathogenic mutation, we broadened the analysis to include all known genes, eventually leading to the identification of a mutation in the XIAP gene. Because XIAP deficiency was not previously known to cause a severe Crohn-like phenotype, we then confirmed the loss of XIAP protein function in the patient’s cells. Having diagnosed the patient with XIAP deficiency, we needed to reorient the clinical approach to address the attendant risks of hemophagocytic lymphohistiocytosis (HLH), regardless of its role in the etiology of the patients inflammatory bowel disease. 2 Accordingly, we evaluated for Epstein-Barr Virus infection (negative to date) and considered approaches to chemoprophylaxis. We reviewed the intestinal pathology and bone marrow specimens, performed a liver biopsy, and established that there was no evidence of active HLH. Nevertheless, the data regarding the natural history of XLP2 suggest that this child had a high probability of death due to HLH in the future, an outcome that could be prevented by hematopoietic stem cell transplant. Therefore, this was the singular basis for the decision to perform a transplant. Furthermore, the link between XIAP and a loss of NOD2 signaling, a pathway implicated in Crohn disease, gave us hope that a transplant could improve the gastrointestinal condition as well.