PPA2-associated sudden cardiac death: extending the clinical and allelic spectrum in 20 new families.

PURPOSE: Biallelic hypomorphic variants in PPA2, encoding the mitochondrial inorganic pyrophosphatase 2 protein, have been recently identified in individuals presenting with sudden cardiac death, occasionally triggered by alcohol intake or a viral infection. Here we report 20 new families harboring PPA2 variants. METHODS: Synthesis of clinical and molecular data concerning 34 individuals harboring five previously reported PPA2 variants and 12 novel variants, 11 of which were functionally characterized. RESULTS: Among the 34 individuals, only 6 remain alive. Twenty-three died before the age of 2 years while five died between 14 and 16 years. Within these 28 cases, 15 died of sudden cardiac arrest and 13 of acute heart failure. One case was diagnosed prenatally with cardiomyopathy. Four teenagers drank alcohol before sudden cardiac arrest. Progressive neurological signs were observed in 2/6 surviving individuals. For 11 variants, recombinant PPA2 enzyme activities were significantly decreased and sensitive to temperature, compared to wild-type PPA2 enzyme activity. CONCLUSION: We expand the clinical and mutational spectrum associated with PPA2 dysfunction. Heart failure and sudden cardiac arrest occur at various ages with inter- and intrafamilial phenotypic variability, and presentation can include progressive neurological disease. Alcohol intake can trigger cardiac arrest and should be strictly avoided.

An autoantibody identifies arrhythmogenic right ventricular cardiomyopathy and participates in its pathogenesis.

Aims: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is characterized by right ventricular myocardial replacement and life-threatening ventricular arrhythmias. Desmosomal gene mutations are sometimes identified, but clinical and genetic diagnosis remains challenging. Desmosomal skin disorders can be caused by desmosomal gene mutations or autoantibodies. We sought to determine if anti-desmosome antibodies are present in subjects with ARVC. Methods and results: We evaluated ARVC subjects and controls for antibodies to cardiac desmosomal cadherin proteins. Desmoglein-2 (DSG2), desmocollin-2, and N-cadherin proteins on western blots were exposed to sera, in primary and validation cohorts of subjects and controls, as well as the naturally occurring Boxer dog model of ARVC. We identified anti-DSG2 antibodies in 12/12 and 25/25 definite ARVC cohorts and 7/8 borderline subjects. Antibody was absent in 11/12, faint in 1/12, and absent in 20/20 of two control cohorts. Anti-DSG2 antibodies were present in 10/10 Boxer dogs with ARVC, and absent in 18/18 without. In humans, the level of anti-DSG2 antibodies correlated with the burden of premature ventricular contractions (r = 0.70), and antibodies caused gap junction dysfunction, a common feature of ARVC, in vitro. Anti-DSG2 antibodies were present in ARVC subjects regardless of whether an underlying mutation was identified, or which mutation was present. A disease-specific DSG2 epitope was identified. Conclusion: Anti-DSG2 antibodies are a sensitive and specific biomarker for ARVC. The development of autoimmunity as a result of target-related mutations is unique. Anti-DSG2 antibodies likely explain the cardiac inflammation that is frequently identified in ARVC and may represent a new therapeutic target.

Mutations in the genes for thyroglobulin and thyroid peroxidase cause thyroid dyshormonogenesis and autosomal-recessive intellectual disability.

We have used single-nucleotide polymorphism microarray genotyping and homozygosity-by-descent (HBD) mapping followed by Sanger sequencing or whole-exome sequencing (WES) to identify causative mutations in three consanguineous families with intellectual disability (ID) related to thyroid dyshormonogenesis (TDH). One family was found to have a shared HBD region of 12.1 Mb on 8q24.21-q24.23 containing 36 coding genes, including the thyroglobulin gene, TG. Sanger sequencing of TG identified a homozygous nonsense mutation Arg2336*, which segregated with the phenotype in the family. A second family showed several HBD regions, including 6.0 Mb on 2p25.3-p25.2. WES identified a homozygous nonsense mutation, Glu596*, in the thyroid peroxidase gene, TPO. WES of a mother/father/proband trio from a third family revealed a homozygous missense mutation, Arg412His, in TPO. Mutations in TG and TPO are very rarely associated with ID, mainly because TDH is generally detectable and treatable. However, in populations where resources for screening and detection are limited, and especially where consanguineous marriages are common, mutations in genes involved in thyroid function may also be causes of ID, and as TPO and TG mutations are the most common genetic causes of TDH, these are also likely to be relatively common causes of ID.

Identification of a homozygous missense mutation in LRP2 and a hemizygous missense mutation in TSPYL2 in a family with mild intellectual disability.

Non-syndromic autosomal recessive intellectual disability (ID) is a genetically heterogeneous disorder with more than 50 mutated genes to date. ID is characterized by deficits in memory skills and language development with difficulty in learning, problem solving, and adaptive behaviors, and affects ∼ 1% of the population. For detection of disease-causing mutations in such a heterogeneous disorder, homozygosity mapping together with exome sequencing is a powerful approach, as almost all known genes can be assessed simultaneously in a high-throughput manner. In this study, a hemizygous c.786C>G:p.Ile262Met in the testis specific protein Y-encoded-like 2 (TSPYL2) gene and a homozygous c.11335G>A:p.Asp3779Asn in the low-density lipoprotein receptor-related protein 2 (LRP2) gene were detected after genome-wide genotyping and exome sequencing in a consanguineous Pakistani family with two boys with mild ID. Mutations in the LRP2 gene have previously been reported in patients with Donnai-Barrow and Stickler syndromes. LRP2 has also been associated with a 2q locus for autism (AUTS5). The TSPYL2 variant is not listed in any single-nucleotide polymorphism databases, and the LRP2 variant was absent in 400 ethnically matched healthy control chromosomes, and is not listed in single-nucleotide polymorphism databases as a common polymorphism. The LRP2 mutation identified here is located in one of the low-density lipoprotein-receptor class A domains, which is a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism, suggesting that alteration of cholesterol processing pathway can contribute to ID.

Disruption of the methyltransferase-like 23 gene METTL23 causes mild autosomal recessive intellectual disability.

We describe the characterization of a gene for mild nonsyndromic autosomal recessive intellectual disability (ID) in two unrelated families, one from Austria, the other from Pakistan. Genome-wide single nucleotide polymorphism microarray analysis enabled us to define a region of homozygosity by descent on chromosome 17q25. Whole-exome sequencing and analysis of this region in an affected individual from the Austrian family identified a 5 bp frameshifting deletion in the METTL23 gene. By means of Sanger sequencing of METTL23, a nonsense mutation was detected in a consanguineous ID family from Pakistan for which homozygosity-by-descent mapping had identified a region on 17q25. Both changes lead to truncation of the putative METTL23 protein, which disrupts the predicted catalytic domain and alters the cellular localization. 3D-modelling of the protein indicates that METTL23 is strongly predicted to function as an S-adenosyl-methionine (SAM)-dependent methyltransferase. Expression analysis of METTL23 indicated a strong association with heat shock proteins, which suggests that these may act as a putative substrate for methylation by METTL23. A number of methyltransferases have been described recently in association with ID. Disruption of METTL23 presented here supports the importance of methylation processes for intact neuronal function and brain development.

Towards a comprehensive structural variation map of an individual human genome.

BACKGROUND: Several genomes have now been sequenced, with millions of genetic variants annotated. While significant progress has been made in mapping single nucleotide polymorphisms (SNPs) and small (<10 bp) insertion/deletions (indels), the annotation of larger structural variants has been less comprehensive. It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions. RESULTS: We have combined computational re-analysis of existing whole genome sequence data with novel microarray-based analysis, and detect 12,178 structural variants covering 40.6 Mb that were not reported in the initial sequencing of the first published personal genome. We estimate a total non-SNP variation content of 48.8 Mb in a single genome. Our results indicate that this genome differs from the consensus reference sequence by approximately 1.2% when considering indels/CNVs, 0.1% by SNPs and approximately 0.3% by inversions. The structural variants impact 4,867 genes, and >24% of structural variants would not be imputed by SNP-association. CONCLUSIONS: Our results indicate that a large number of structural variants have been unreported in the individual genomes published to date. This significant extent and complexity of structural variants, as well as the growing recognition of their medical relevance, necessitate they be actively studied in health-related analyses of personal genomes. The new catalogue of structural variants generated for this genome provides a crucial resource for future comparison studies.

Differential outcomes in 3 types of acute antibody-mediated rejection.

INTRODUCTION: The aim of this study is to investigate the prevalence, predictors, and clinical outcomes of acute antibody-mediated rejection (AAMR). METHODS: Retrospective analysis of 833 adult patients who received kidney transplantation between 1/1/2001 and 8/15/2007. RESULTS: The prevalence of AAMR and acute cellular rejection was 2% and 8.2%, respectively. Eight patients had type I, seven type II, and two type III AAMR. All patients had at least one strong donor-specific anti-HLA antibodies (DSA) with a median fluorescence intensity (MFI) value of over 6000 and the mean number of strong DSAs was 2.0 +/- 0.7. Fifteen of 17 patients received pre-transplant desensitization treatment. During a median 28 months of follow-up (range: 12-38 months), two patients died (88% patient survival), and nine lost their allografts (35% graft survival). While all type I AAMR patients responded to treatment, all type III patients, and four of seven patients with type II AAMR lost their allografts earlier, and three type II AAMR patients later due to transplant glomerulopathy. CONCLUSIONS: AAMR is mainly seen in patients with pre-transplant strong DSAs. There is a striking difference in clinical outcomes of AAMR that types II and III AAMR patients have poor prognosis compared to type I AAMR patients.

Intragenic deletions in the dystrophin gene in 211 Pakistani Duchenne muscular dystrophy patients.

BACKGROUND: Deletions of single or multiple exonic regions within the dystrophin gene can be detected using current molecular methods in approximately 65% of the patients with X-linked recessive neuromuscular disorder, Duchenne/Becker muscular dystrophy (DMD/BMD). Population-based variations in frequency and distribution of dystrophin gene deletions have been reported in DMD/BMD patients. In the present study, the first in the Pakistani population, frequency and distribution of deletions of 18 exons clustered in two hot spots within the dystrophin gene in 211 unrelated DMD patients were analyzed. METHODS: A total of 211 patients suffering from DMD were ascertained, and intragenic deletions within the dystrophin gene were detected on polymerase chain reaction amplification of the genomic DNA using 18 primer sets clustered within two major deletion hot spots. lovd v.1.1.0 software from the Leiden Muscular Dystrophy website has been used to predict in-frame and out-of-frame deletions. RESULTS: Intragenic deletions were detected in 86 patients (40.75%): 35 patients (40.69%) had deletions within the proximal hot spot, and 51 patients (59.30%) had deletions confined to the distal deletion hot spot of the dystrophin gene. The most frequently deleted exons were 50, 6, 47, 13 and 52 with deletion frequencies of 15.11%, 12.79%, 10.46%, 8.13%, and 4.65%, respectively. lovd v.1.1.0 predicted out-of-frame deletions in 67 DMD patients and in-frame deletions in 19 DMD patients. CONCLUSIONS: The observed proportion of intragenic deletions in the Pakistani population is relatively low, which is comparable with most of the Asian data. Also, deletions in 67 patients (77.9%) are in agreement with the frame-shift rule.

Pulmonary hypertension in peritoneal dialysis patients.

The information available in the literature regarding pulmonary hypertension (PH) in peritoneal dialysis (PD) patients is limited. The objective of the present study was to examine the prevalence and characteristics of PH in PD patients. We retrospectively collected the clinical profile, echocardiographic (ECHO) findings, and biochemical data for 36 PD patients for which ECHO findings were available. We compared characteristics between patients with and without PH. We found PH, defined as pulmonary arterial pressure (PAP) > or = 35 mmHg, in 15 patients. The prevalence of PH was 42%. Mean age (+/- standard deviation) of the patients with and without PH was 58 +/- 15 years and 52 +/- 15 years respectively (p = 0.30). Mean PAP of the PH patients was 43.8 +/- 9.0 mmHg (range: 35-65 mmHg). Patients with PH had a lower ejection fraction than did patients without PH (46.3% +/- 19.8% vs. 56.5% +/- 11.8% respectively, p = 0.07). Patients with PH also had a higher prevalence of global hypokinesia (60% vs. 29%, p = 0. 059) and dilated left ventricular chamber (53% vs. 19%, p = 0.03). In PH patients, body mass index (24 +/- 4.5 kg/m2 vs. 28 +/- 5.0 kg/m2, p = 0.024), normalized protein catabolic rate (0. 78 +/- 0.21 g/kg vs. 0.95 +/- 0.27 g/kg daily, p = 0.049), and ferritin (226 +/- 210 ng/mL vs. 873 +/- 965 ng/mL, p = 0.005) were significantly lower and lactate dehydrogenase was higher (264 +/- 99 U/L vs. 206 +/- 79 U/L, p = 0.06) than in patients without PH. We observed no significant differences in race or sex, incidence of hypertension or cardiovascular disease, or vitamin D analog use between the two groups of patients. During the study period, 60% of PH patients and 38% of patients without PH died (p = 0.19). Values of PAP correlated directly with serum levels of phosphorus (r = 0.44, p = 0.02), CaxP product (r = 0.40, p = 0.04), and parathyroid hormone (r = 0.42, p = 0.03). Of continuous ambulatory PD and continuous cycling PD patients, 21% and 55% respectively had PH (p = 0. 049). In PD patients, PH is highly prevalent and may be associated with higher mortality risk.

Candida parapsilosis endocarditis 8 months after transient candidemia.

We report a case of aortic valve endocarditis with aortic root abscess from Candida parapsilosis occurring 8 months after transient candidemia. Despite the fact that the patient was treated appropriately, candidemia persisted and later on presented with an embolic stroke as a complication of fungal endocarditis.

Genome assembly comparison identifies structural variants in the human genome.

Numerous types of DNA variation exist, ranging from SNPs to larger structural alterations such as copy number variants (CNVs) and inversions. Alignment of DNA sequence from different sources has been used to identify SNPs and intermediate-sized variants (ISVs). However, only a small proportion of total heterogeneity is characterized, and little is known of the characteristics of most smaller-sized (<50 kb) variants. Here we show that genome assembly comparison is a robust approach for identification of all classes of genetic variation. Through comparison of two human assemblies (Celera's R27c compilation and the Build 35 reference sequence), we identified megabases of sequence (in the form of 13,534 putative non-SNP events) that were absent, inverted or polymorphic in one assembly. Database comparison and laboratory experimentation further demonstrated overlap or validation for 240 variable regions and confirmed >1.5 million SNPs. Some differences were simple insertions and deletions, but in regions containing CNVs, segmental duplication and repetitive DNA, they were more complex. Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects.

Relationship of peritoneal transport rate and dialysis adequacy with inflammation in peritoneal dialysis patients.

Inflammation, dialysis adequacy, and peritoneal transport rate (PTR) influence clinical outcomes in peritoneal dialysis (PD) patients. The present study examined the relationship of C-reactive protein (CRP), a marker of inflammation, to PTR and residual renal function (RRF) in PD patients. We recorded the baseline dialysate-to-plasma creatinine (D/P Cr) of 210 PD patients starting in 1986. In a subgroup of 42 patients, we serially measured high-sensitivity CRP levels and.dialysis adequacy, including weekly Kt/V urea and creatinine clearance (CCr), starting in May 2003. The patients were followed to January 2006. Mean age was 53 +/- 16 (standard deviation) years, and 70% of the patients were African American. Enrollment mean and median CRP levels were 13.53 +/- 20.8 (range: 0.2-95.8) and 7.15 mg/L respectively. Mean weekly residual CCr and Kt/V during follow-up were 7.11 +/- 15.47 L/1.73 m2 and 0.14 +/- 0.30 respectively. The mean enrollment D/P Cr was 0.649 +/- 0.12 (range: 0.429-0.954). Patients with CRP > 10 mg/L had significantly lower weekly residual CCr (0.59 L/1.73 m2 vs. 10.1 L/1.73 m2, p = 0.01), residual Kt/V (0.01 vs. 0.20, p = 0.01), total CCr (56 L/1.73 m2 vs. 62 L/1.73 m2, p= 0.047), and total Kt/V (2.09 vs. 2.49, p = 0.001) than did those with CRP < or = 10 mg/L. Levels of CRP correlated negatively with weekly residual CCr (r = -0.42, p = 0.006), residual Kt/V (r = -0.43, p = 0.006), and total Kt/V (r = -0.44, p = 0.004). Enrollment D/P Cr was inversely correlated with serum albumin (r = -0.24, p = 0.001) and directly correlated with peritoneal protein loss (r = 0.34, p = 0.028). Higher enrollment D/P Cr was associated with lower observed cumulative survival (Kaplan-Meier) in PD patients. However D/P Cr was not an independent predictor of long-term survival in PD patients. Using multivariate Cox regression analysis, and including D/P Cr and residual Kt/V in the model, enrollment CRP was an independent predictor of mortality (relative risk = 1.036, p = 0.018). We conclude that elevated CRP is associated with lower RRF As a predictor of mortality, CRP may be better than RRF and D/P Cr.