Cryptococcus neoformans osteomyelitis and intramuscular abscess in a liver transplant patient.

BMJ Case Rep. 2017 Oct 11;2017:

Authors: Poenaru SM, Rofaiel R, Hosseini-Moghaddam SM

Abstract
Cryptococcus neoformans is an important pathogen that can cause severe illness and mortality in immunocompromised patients. We highlight here the case of a 53-year-old man presenting to hospital 4 years postliver transplant with fever, acute renal failure and a medial thigh lesion. Initially treated as bacterial sepsis, the patient failed to improve on broad-spectrum antibiotics. Further investigations revealed disseminated cryptococcemia complicated by patellar osteomyelitis and an intramuscular abscess. Unfortunately, although the patient initially showed signs of clinical improvement after starting standard antifungal agents, he deteriorated and died secondary to acute renal failure. Osteomyelitis is a rare manifestation of cryptococcal infection for which there is often a significant delay to diagnosis and treatment. This is the fourth reported case of cryptococcal osteomyelitis in a liver transplant patient and underlines the importance of considering fungal infections in the differential diagnosis of osseous lesions in solid organ transplant and other immunocompromised patients.

PMID: 29025780 [PubMed - indexed for MEDLINE]

Erdheim-Chester disease: atypical presentation of a rare disease.

BMJ Case Rep. 2017 Oct 11;2017:

Authors: Calandra CR, Bustos A, Falcon F, Arakaki N

Abstract
We report the clinical case of an adult patient referred to our hospital because of trismus due to a tumour in the right infratemporal and pterygomaxillary fossa. He referred hyporexia, weight loss and right trigeminal neuralgia. On physical examination, he had trismus and diplopia. On neuroimaging, the tumour invaded the central nervous system affecting the right temporal lobe and orbit, and the sellar region. Tumour biopsy revealed foamy histiocytes and isolated giant multinuclear cells immunoreactive to CD68 and negative to CD1a and S100. A diagnosis of Erdheim-Chester disease was made. Non-evidence of large bone involvement was found in neither plain radiographs nor Technetium 99 m bone scintigraphy. BRAFV600E mutation analysis was negative. Because of raised intracranial pressure, a debulking surgery of the intracranial histiocytic process was performed. The patient improved his symptoms and remains clinically stable after 12 months of treatment with pegylated interferon-α-2a 180 µg/weekly.

PMID: 29025773 [PubMed - indexed for MEDLINE]

Single giant mediastinal rhabdomyoma as a sole manifestation of TSC in foetus.

Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2017 Sep;161(3):326-329

Authors: Godava M, Filipova H, Dubrava L, Vrtel R, Michalkova K, Janikova M, Bakaj-Zbrozkova L, Navratil J

Abstract
BACKGROUND: Presence of multiple cardiac rhabdomyomas is one of the major features of Tuberous sclerosis (TSC), but isolated progressing single giant rhabdomyoma is very rare and not typical of TSC.
CASE REPORT: This report presents family without obvious history of TSC with occurrence of giant mediastinal rhabdomyoma affecting the haemodynamics in male foetus, without other TSC symptoms. Girl from the next gravidity had prenatally detected multiple rhabdomyomas and small subcortical tuber of brain detected after birth. DNA analysis found novel c.4861A>T TSC2 variant and large deletion in TSC2 in tumour tissue from male foetus. The novel TSC2 variant was also present in the girl and her healthy father, in silico analysis suggested its functional effect on TSC2. Brain MRI of the father detected mild TSC specific abnormality.
CONCLUSION: We suggest the novel TSC2 mutation is a cause of mild TSC in this family and has reduced expression. The clinical and molecular findings in this family also emphasize that TSC diagnosis should be also evaluated in case of single giant foetal cardiac rhabdomyoma.

PMID: 28659645 [PubMed - indexed for MEDLINE]

Triple jeopardy for people with albinism.

Pigment Cell Melanoma Res. 2016 09;29(5):487

Authors: Arnheiter H, Long G, Aplin A, Harris J, Kelsh R

PMID: 27615283 [PubMed - indexed for MEDLINE]

Knowledge will Propel Machine Understanding of Content: Extrapolating from Current Examples.

Proc IEEE WIC ACM Int Conf Web Intell Intell Agent Technol. 2017 Aug;2017:1-9

Authors: Sheth A, Perera S, Wijeratne S, Thirunarayan K

Abstract
Machine Learning has been a big success story during the AI resurgence. One particular stand out success relates to learning from a massive amount of data. In spite of early assertions of the unreasonable effectiveness of data, there is increasing recognition for utilizing knowledge whenever it is available or can be created purposefully. In this paper, we discuss the indispensable role of knowledge for deeper understanding of content where (i) large amounts of training data are unavailable, (ii) the objects to be recognized are complex, (e.g., implicit entities and highly subjective content), and (iii) applications need to use complementary or related data in multiple modalities/media. What brings us to the cusp of rapid progress is our ability to (a) create relevant and reliable knowledge and (b) carefully exploit knowledge to enhance ML/NLP techniques. Using diverse examples, we seek to foretell unprecedented progress in our ability for deeper understanding and exploitation of multimodal data and continued incorporation of knowledge in learning techniques.

PMID: 29962511 [PubMed]

Correction: Endonuclease G promotes mitochondrial genome cleavage and replication.

Oncotarget. 2018 Jun 12;9(45):27908

Authors: Wiehe RS, Gole B, Chatre L, Walther P, Calzia E, Palmer A, Gebhardt JCM, Ricchetti M, Wiesmüller L

Abstract
[This corrects the article DOI: 10.18632/oncotarget.24822.].

PMID: 29963248 [PubMed - in process]

Comparative Study of Wheatley's Trichrome Stain and In-vitro Culture against PCR Assay for the Diagnosis of Blastocystis sp. in Stool Samples.

Iran J Parasitol. 2018 Jan-Mar;13(1):127-136

Authors: Mohammad NA, Mastuki MF, Al-Mekhlafi HM, Moktar N, Anuar TS

Abstract
Background: This study evaluated the performance of routine permanent stain and cultivation method in comparison with polymerase chain reaction assay as the reference technique to detect Blastocystis sp.
Methods: A cross-sectional study was conducted among aboriginal populations that reside in Pahang, Peninsular Malaysia in Feb to Mar 2015. A total of 359 stool samples were examined using Wheatley's trichrome stain, in-vitro cultivation in Jones' medium and PCR assay. Positive amplicons were subjected to sequencing and phylogenetic analysis.
Results: Fifty-six (15.6%) samples were detected positive with Blastocystis sp. by Wheatley's trichrome stain and 73 (20.3%) by in-vitro culture, while PCR assay detected 71 (19.8%) positive samples. Detection rate of Blastocystis sp. was highest in combination of microscopic techniques (27.9%). The sensitivity and specificity of Wheatley's trichrome staining and in-vitro culture techniques compared to PCR assay were 49.3% (95% CI: 37.2-61.4) and 92.7% (95% CI: 89.1-95.4) and 39.4% (95% CI: 28.0-51.8) and 84.4% (95% CI: 79.7-88.4), respectively. However, the sensitivity [60.6% (95% CI: 48.3-71.9)] of the method increased when both microscopic techniques were performed together. False negative results produced by microscopic techniques were associated with subtype 3. The agreement between Wheatley's trichrome stain, in-vitro culture and combination of microscopic techniques with PCR assay were statistically significant by Kappa statistics (Wheatley's trichrome stain: K = 0.456, P<0.001; in-vitro culture: K = 0.236, P<0.001 and combination techniques: K = 0.353, P<0.001).
Conclusion: The combination of microscopic technique is highly recommended to be used as a screening method for the diagnosis of Blastocystis infection either for clinical or epidemiological study to ensure better and accurate diagnosis.

PMID: 29963095 [PubMed]

Temozolomide and Pituitary Tumors: Current Understanding, Unresolved Issues, and Future Directions.

Front Endocrinol (Lausanne). 2018;9:318

Authors: Syro LV, Rotondo F, Camargo M, Ortiz LD, Serna CA, Kovacs K

Abstract
Temozolomide, an alkylating agent, initially used in the treatment of gliomas was expanded to include pituitary tumors in 2006. After 12 years of use, temozolomide has shown a notable advancement in pituitary tumor treatment with a remarkable improvement rate in the 5-year overall survival and 5-year progression-free survival in both aggressive pituitary adenomas and pituitary carcinomas. In this paper, we review the mechanism of action of temozolomide as alkylating agent, its interaction with deoxyribonucleic acid repair systems, therapeutic effects in pituitary tumors, unresolved issues, and future directions relating to new possibilities of targeted therapy.

PMID: 29963012 [PubMed]

Economic Evaluation of Implementing a Novel Pharmacogenomic Test (IDgenetix®) to Guide Treatment of Patients with Depression and/or Anxiety.

Pharmacoeconomics. 2017 Dec;35(12):1297-1310

Authors: Najafzadeh M, Garces JA, Maciel A

Abstract
BACKGROUND: The response to therapeutics varies widely in patients with depression and anxiety, making selection of an optimal treatment choice challenging. IDgenetix®, a novel pharmacogenomic test, has been shown to improve outcomes by predicting the likelihood of response to different psychotherapeutic medications.
OBJECTIVE: The objective of this study was to estimate the cost effectiveness of implementing a novel pharmacogenomic test (IDgenetix®) to guide treatment choices in patients with depression and/or anxiety compared with treatment as usual from the US societal perspective.
METHODS: We developed a discrete event simulation to compare clinical events, quality-adjusted life-years, and costs of the two treatment strategies. Target patients had a Hamilton Rating Scale for Depression Score ≥ 20 and/or a Hamilton Rating Scale for Anxiety score ≥ 18 at baseline. Remission, response, and no response were simulated based on the observed rates in the IDgenetix® randomized controlled trial. Quality-adjusted life-years and direct and indirect costs attributable to depression and anxiety were estimated and compared over a 3-year time horizon. We conducted extensive deterministic and probabilistic sensitivity analyses to assess the robustness of the results.
RESULTS: The model predicted cumulative remission rates of 78 and 66% in IDgenetix® and treatment as usual groups, respectively. Estimated discounted quality-adjusted life-years were 2.09 and 1.94 per patient for IDgenetix® and treatment as usual, respectively, which resulted in 0.15 incremental quality-adjusted life-years (95% credible interval 0.04-0.28). The total costs after accounting for a US$2000 test cost were US$14,124 for IDgenetix® compared with US$14,659 for treatment as usual, suggesting a US$535 (95% credible interval - 2902 to 1692) cost saving per patient in the IDgenetix® group. Incremental quality-adjusted life-year gain (0.49) and cost savings (US$6800) were substantially larger in patients with severe depression (Hamilton Rating Scale for Depression score ≥ 25).
CONCLUSION: Using the IDgenetix® test to guide the treatment of patients with depression and anxiety may be a dominant strategy, as it improves quality-adjusted life-years and decreases overall costs over a 3-year time horizon.

PMID: 29110140 [PubMed - indexed for MEDLINE]

Environmental exposure to organophosphorus nerve agents.

Environ Toxicol Pharmacol. 2017 Dec;56:163-171

Authors: Vucinic S, Antonijevic B, Tsatsakis AM, Vassilopoulou L, Docea AO, Nosyrev AE, Izotov BN, Thiermann H, Drakoulis N, Brkic D

Abstract
Exposure to organophosphorus nerve agents, the most deadly chemical warfare agents, is possible in a variety of situations, such as destruction of chemical warfare agents, terrorist attacks, armed conflicts or accidents in research laboratories and storage facilities. Hundreds of thousands of tons of chemical munitions were disposed of at the sea in the post World War II period, with European, Russian, Japanese and US coasts being the most affected. Sulfur mustard, Lewisite and nerve agents appear to be the most frequently chemical warfare agents disposed of at the sea. Addressing the overall environmental risk, it has been one of the priorities of the world community since that time. Aside from confirming exposure to nerve agents in the alleged use for forensic purposes, the detection and identification of biological markers of exposure are also needed for the diagnosis and treatment of poisoning, in addition to occupational health monitoring for specific profiles of workers. When estimating detrimental effects of acute or potential chronic sub-lethal doses of organophosphorus nerve agents, released accidentally or intentionally into the environment, it is necessary to understand the wide spectra of physical, chemical and toxicological properties of these agents, and predict their ultimate fate in environmental systems.

PMID: 28942081 [PubMed - indexed for MEDLINE]

Long-term outcomes of elderly patients with CYP2C9 and VKORC1 variants treated with vitamin K antagonists.

J Thromb Haemost. 2017 Nov;15(11):2165-2175

Authors: Nagler M, Angelillo-Scherrer A, Méan M, Limacher A, Abbal C, Righini M, Beer JH, Osterwalder J, Frauchiger B, Aschwanden M, Matter CM, Kucher N, Cornuz J, Banyai M, Husmann M, Staub D, Mazzolai L, Hugli O, Rodondi N, Aujesky D

Abstract
Essentials The long-term effects of VKORC1 and CYP2C9 variants on clinical outcomes remains unclear. We followed 774 patients ≥65 years with venous thromboembolism for a median duration of 30 months. Patients with CYP2C9 variants are at increased risk of death and non-major bleeding. Patients with genetic variants have a slightly lower anticoagulation quality only.
SUMMARY: Background The long-term effect of polymorphisms of the vitamin K-epoxide reductase (VKORC1) and the cytochrome P450 enzyme gene (CYP2C9) on clinical outcomes remains unclear. Objectives We examined the association between CYP2C9/VKORC1 variants and long-term clinical outcomes in a prospective cohort study of elderly patients treated with vitamin K antagonists for venous thromboembolism (VTE). Methods We followed 774 consecutive patients aged ≥ 65 years with acute VTE from nine Swiss hospitals for a median duration of 30 months. The median duration of initial anticoagulant treatment was 9.4 months. The primary outcome was the time to any clinical event (i.e. the composite endpoint of overall mortality, major and non-major bleeding, and recurrent VTE. Results Overall, 604 (78%) patients had a CYP2C9 or VKORC1 variant. Three hundred and thirty-four patients (43.2%) had any clinical event, 119 (15.4%) died, 100 (12.9%) had major and 167 (21.6%) non-major bleeding, and 100 had (12.9%) recurrent VTE. After adjustment, CYP2C9 (but not VKORC1) variants were associated with any clinical event (hazard ratio [HR], 1.34; 95% confidence interval [CI], 1.08-1.66), death (HR, 1.74; 95% CI, 1.19-2.52) and clinically relevant non-major bleeding (sub-hazard ratio [SHR], 1.39; 95% CI, 1.02-1.89), but not with major bleeding (SHR, 1.03; 95% CI, 0.69-1.55) or recurrent VTE (SHR, 0.95; 95% CI, 0.62-1.44). Patients with genetic variants had a slightly lower anticoagulation quality. Conclusions CYP2C9 was associated with long-term overall mortality and non-major bleeding. Although genetic variants were associated with a slightly lower anticoagulation quality, there was no relationship between genetic variants and major bleeding or VTE recurrence.

PMID: 28834238 [PubMed - indexed for MEDLINE]

PHARMACOKINETIC STUDY OF CONVERSION BETWEEN TWO FORMULATIONS OF ONCE-DAILY EXTENDED-RELEASE TACROLIMUS IN STABLE LUNG TRANSPLANT PATIENTS.

Transplantation. 2018 Jun 29;:

Authors: Sintes H, Sáez-Giménez B, Berastegui C, López-Meseguer M, Monforte V, Bravo C, Vima J, Gómez-Ollés S, Roman A

Abstract
BACKGROUND: The aim of this study was to compare the pharmacokinetic profile, tolerability, and safety of a novel once-daily extended-release formulation of tacrolimus (LCPT) with that of once-daily prolonged-release tacrolimus (ODT) in stable adult lung transplant (LT) recipients.
METHODS: Phase II, open-label, single-arm, single-center, prospective pilot pharmacokinetic study. Study population comprised 20 stable LTR receiving ODT, mean age 55.9 (r: 38-67) years, 13 (65%) men. Patients were switched to LCPT in a 1:0.7 (mg/mg) conversion dose. Follow-up was 6 months, and cystic fibrosis patients were excluded. Two 24-hour pharmacokinetic profiles were obtained for each patient, the first on day -14 and the second on day +14 after switching to LCPT. Pharmacokinetic parameters and safety were compared.
RESULTS: Mean (SD) AUC0-24 was 253.97 (61.90) ng/mL/h for ODT and 282.44 (68.2) ng/mL/h for LCPT. Systemic exposure was similar in both (Schuirmann two 1-sided test). Mean (SD) dose was 5.05 (1.67) mg in ODT and 3.36 (1.03) mg in LCPT (p: 0.0002). Time to maximum concentration was 125 minutes for ODT and 325 minutes for LCPT (p<0.001). Correlation between AUC0-24 and C24 was 0.896 (r) for ODT and 0.893 (r) for LCPT. There were no differences in adverse effects. At 6 months, conversion dose was 1:0.59 (mg/mg) in patients with unchanged Cmin target levels.
CONCLUSIONS: Switching from ODT to LCPT was safe and well tolerated in stable LT recipients without cystic fibrosis. A significantly lower dose of LCPT allows similar bioavailability. A conversion ratio 1:0.6 could be enough to maintain similar target levels.

PMID: 29965950 [PubMed - as supplied by publisher]

Antifibrinolytic therapy for preventing oral bleeding in people on anticoagulants undergoing minor oral surgery or dental extractions.

Cochrane Database Syst Rev. 2018 Jul 02;7:CD012293

Authors: Engelen ET, Schutgens RE, Mauser-Bunschoten EP, van Es RJ, van Galen KP

Abstract
BACKGROUND: Individuals on continuous treatment with vitamin K antagonists (VKAs) or direct oral anticoagulants (DOACs) are at increased risk of bleeding complications during and after oral or dental procedures. Anticoagulant treatment is preferably continued at the same dose, since dose reduction or discontinuation of treatment is associated with an increased risk of thromboembolism. The use of haemostatic measures during or after the procedure (or both) could enable continuation of the oral anticoagulant treatment.
OBJECTIVES: We aimed to assess the efficacy of antifibrinolytic agents for preventing bleeding complications in people on oral anticoagulants undergoing minor oral surgery or dental extractions.
SEARCH METHODS: We searched the Cochrane Cystic Fibrosis and Genetic Disorders Coagulopathies Trials Register, compiled from electronic database searches and handsearching of journals and conference abstract books. We also searched the reference lists of relevant articles and reviews. We searched PubMed, Embase and the Cochrane Library. Additional searches were performed using ClinicalTrials.gov, the International Clinical Trials Registry Platform (ICTRP), the CINAHL database of nursing and allied health services, the open access ProQuest dissertation database, papers and reports from the American College of Clinical Pharmacy (ACCP) and abstract books from annual scientific conferences.Date of last search: 04 January 2018.
SELECTION CRITERIA: Randomised and quasi-randomised controlled trials in people on continuous treatment with VKAs or DOACs undergoing oral or dental procedures using antifibrinolytic agents (tranexamic acid (TXA) or epsilon aminocaproic acid) to prevent perioperative bleeding compared to no intervention or usual care with or without placebo.
DATA COLLECTION AND ANALYSIS: Two authors independently screened the titles and abstracts of all identified articles. Full texts were obtained from potentially relevant abstracts and two authors independently assessed these for inclusion based of the selection criteria. A third author verified trial eligibility. Two authors independently performed data extraction and risk of bias assessments using standardized forms. The quality of the evidence was assessed using GRADE.
MAIN RESULTS: No eligible trials in people on continuous treatment with DOACs undergoing oral or dental procedures were identified.Three randomised trials and one quasi-randomised trial (follow-up in all was seven days) in people on continuous treatment with VKAs were included with a total of 253 participants (mean age 60 years). Two trials published in 1989 and 1993 compared the antifibrinolytic agent TXA with placebo in people using VKAs. Two other trials were published in 1999 and 2015 and compared TXA with gelatin sponge and sutures, and dry gauze compression, respectively. In all included trials, those who were treated with VKAs had international normalised ratio (INR) values within the therapeutic range and TXA was applied locally, not systemically.The two trials from 1989 and 1993 comparing TXA with placebo showed a statistically significant beneficial effect regarding the number of major postoperative bleeding episodes requiring intervention, with a pooled risk difference (RD) of -0.25 (95% confidence interval (CI) -0.36 to -0.14) (128 participants) (moderate-quality evidence). For the two trials that compared TXA with either gelatin sponge and sutures or with dry gauze compression, there was no difference between the TXA and the standard care group, RD 0.02 (95% CI -0.07 to 0.11) (125 participants) (moderate-quality evidence). The combined RD of all included trials was -0.13 (95% CI -0.30 to 0.05) (moderate-quality evidence). There were no side effects of antifibrinolytic therapy that required treatment withdrawal (128 participants) (moderate-quality evidence). Despite heterogeneity between trials with respect to the different haemostatic measures used in the control groups, the trials were comparable regarding design and baseline participant characteristics.Overall, we considered the risk of bias to be low in the trials comparing TXA with placebo and moderate in the trials comparing TXA with alternative haemostatic measures.
AUTHORS' CONCLUSIONS: Based on the results of this Cochrane Review, there seems to be a beneficial effect of locally applied TXA in preventing oral bleeding in people on continuous treatment with VKAs undergoing minor oral surgery or dental extractions. However, the small number of identified randomised controlled trials, the relatively small number of participants included in the trials and the differences in standard therapy and treatment regimens between trials, do not allow us to conclude definite efficacy of antifibrinolytic therapy in this population.We were unable to identify any eligible trials in people on continuous treatment with DOACs undergoing oral or dental procedures. Therefore, a beneficial effect of antifibrinolytic therapy can currently only be assumed based on data from the people using VKAs.

PMID: 29963686 [PubMed - as supplied by publisher]

Metabolomics: Challenges and Opportunities in Systems Biology Studies.

Methods Mol Biol. 2018;1702:327-336

Authors: Casadei L, Valerio M, Manetti C

Abstract
Metabolomics has the capability of providing predisposition, diagnostic, prognostic, and therapeutic biomarker profiles of individual patients, since a large number of metabolites can be measured in an unbiased manner from biological samples. In this setting, 1H-Nuclear Magnetic Resonance (NMR) spectroscopy of biofluids such as plasma, urine, and fecal water offers the opportunity to identify patterns of biomarker changes that reflects the physiological or pathological status of an individual patient.In this chapter, we show as a metabolomics study can be used to diagnose a disease, classifying patients as healthy or as pathological taking into account individual variability.

PMID: 29119513 [PubMed - indexed for MEDLINE]

Seeing is Engaging: Vlogs as a Tool for Patient Engagement.

Patient. 2017 06;10(3):267-270

Authors: Lee JL, Frey M, Frey P, Hollin IL, Wu AW

PMID: 28101817 [PubMed - indexed for MEDLINE]

A novel missense mutation of CRYGS underlies congenital cataract in a Chinese family.

Gene. 2018 Jun 28;:

Authors: Zhang T, Yan L, Leng Y, Chen C, Ma L, Wang Q, Zhang J, Cao L

Abstract
Congenital cataract is a clinically and genetically heterogeneous disease. In this study, we examined a five-generation Chinese family with autosomal dominant nuclear congenital cataracts by whole exome sequencing. A novel heterozygous missense mutation c.199T>A, p.(Tyr67Asn) in CRYGS was identified in this family. The p.(Tyr67Asn) substitution was predicted to decrease the local hydrophobicity and affect the three-dimensional structure of γS-crystallin, and resulted in a portion of mutant protein translocation from the cytoplasm to cell membrane. Our observations expand the mutation spectrum of CRYGS and provide further evidence for the genetic basis and molecular mechanism of congenital cataract.

PMID: 29964096 [PubMed - as supplied by publisher]

Six novel susceptibility loci for coronary artery disease and cerebral infarction identified by longitudinal exome-wide association studies in a Japanese population.

Biomed Rep. 2018 Aug;9(2):123-134

Authors: Yasukochi Y, Sakuma J, Takeuchi I, Kato K, Oguri M, Fujimaki T, Horibe H, Yamada Y

Abstract
Coronary artery disease (CAD) and cerebral infarction (CI) remain major causes of morbidity and mortality in humans. Recent genome-wide association studies have identified various genetic variants associated with these diseases. However, these studies were commonly conducted in a cross-sectional manner. Therefore, the present research performed longitudinal exome-wide association studies for CAD and CI using data on ~244,000 genotyped variants and the clinical data of 6,026 Japanese individuals who had attended annual health checkups for several years (mean followed-up period, 5±3 years). Following quality controls, the significance [false discovery rate (FDR) of <0.05] of association of the diseases with 24,651 single nucleotide polymorphisms (SNPs) in 5,989 individuals for three inheritance models was tested using the generalized estimating equation model. SNPs that reached statistical significance were further screened against a threshold of approxdf (a scale of small effective sample size) of >30. The longitudinal exome-wide association studies revealed that three SNPs [rs4606855 of ADGRE3 (P=2.5×10-6; FDR=0.031; approxdf=71), rs3746414 of ZFP64 (P=5.9×10-6; FDR=0.048; approxdf=93) and rs7132908 of FAIM2 (P<2.0×10-16; FDR<4.9×10-12; approxdf=65)] were significantly associated with the prevalence of CAD. A different set of three SNPs [rs6580741 of FAM186A (P<2.0×10-16; FDR<4.9×10-12; approxdf=48), rs1324015 of LINC00400 (P<2.0×10-16; FDR<4.9×10-12; approxdf=49) and rs884205 of TNFRSF11A (P<2.0×10-16; FDR<4.9×10-12; approxdf=32)] was significantly associated with CI. The comparison of disease incidence with these SNPs demonstrated that all the minor alleles were associated with decreased susceptibility to CAD or CI. In conclusion, six novel SNPs were identified as susceptibility loci for CAD (rs4606855 of ADGRE3, rs3746414 of ZFP64, and rs7132908 of FAIM2) or CI (rs6580741 of FAM186A, rs1324015 of LINC00400, and rs884205 of TNFRSF11A).

PMID: 29963304 [PubMed]

Population genomics in South East Asia captures unexpectedly high carrier frequency for treatable inherited disorders.

Genet Med. 2018 Jul 02;:

Authors: Bylstra Y, Kuan JL, Lim WK, Bhalshankar JD, Teo JX, Davila S, Teh BT, Rozen S, Tan EC, Liew WKM, Yeo KK, Tan P, SinGapore Incidental Finding (SGIF) study group, Saw SM, Cheng CY, Cook S, Foo R, Jamuar SS

Abstract
PURPOSE: Genomic studies have demonstrated the necessity of ethnicity-specific population data to ascertain variant pathogenicity for disease diagnosis and treatment. This study examined the carrier prevalence of treatable inherited disorders (TIDs), where early diagnosis of at-risk offspring can significantly improve clinical outcomes.
METHODS: Existing exome/ genome sequencing data of 831 Singaporeans were aggregated and examined for disease causing variants in 104 genes associated with 80 TIDs.
RESULTS: Among the 831 Singaporean participants, genomic variant filtering and analysis identified 1 in 18 individuals (6%) to be carriers amongst one of 13 TIDs. Citrin deficiency and Wilson disease had the highest carrier frequency of 1 in 41, and 1 in 103 individuals, respectively. The pathogenic variants associated with citrin deficiency were 24 times more prevalent in our local cohorts when compared to Western cohorts.
CONCLUSION: This study demonstrates the value of a population specific genomic database to determine true disease prevalence and has enabled the discovery of carrier frequencies of treatable genetic conditions specific to South East Asian populations, which are currently underestimated in existing data sources. This study framework can be adapted to other population groups and expanded to multiple genetic conditions to inform health policies directing precision medicine.

PMID: 29961769 [PubMed - as supplied by publisher]

Beyond the panel: preconception screening in consanguineous couples using the TruSight One "clinical exome".

Genet Med. 2018 Jul 02;:

Authors: Kirk EP, Barlow-Stewart K, Selvanathan A, Josephi-Taylor S, Worgan L, Rajagopalan S, Cowley MJ, Gayevskiy V, Bittles A, Burnett L, Elakis G, Lo W, Buckley M, Colley A, Roscioli T

Abstract
PURPOSE: To provide proof of concept by broadening preconception screening beyond targeted testing to inform reproductive risk in consanguineous couples.
METHODS: Consanguineous couples were screened for autosomal recessive and X-linked disorders using the TruSight One panel of 4,813 genes associated with human disease.
RESULTS: We recruited 22 couples, of whom 15 elected to have sequencing. We found four couples to be at risk of autosomal recessive disorders, including one with a child affected by Poretti-Boltshauser syndrome (a diagnosis not made prior to the study) and another previously known to carry a β-globin variant. Two couples were found to carry variants unrelated to known family history. These variants were in the genes C5orf42 (associated with Joubert syndrome and orofaciodigital syndrome) and GYS2 (associated with glycogen synthase deficiency). One known variant was not detected-a single exon deletion in FAM20C. We would not expect to identify this variant with the methodology employed. Of the four variants identified, only the β-globin variant would have been found using available commercial preconception screening panels.
CONCLUSION: Preconception screening of consanguineous couples for recessive and X-linked disorders using genomic sequencing is practicable, and is likely to detect many more at-risk couples than any targeted panel could achieve. A couples-based approach greatly reduces the associated analysis and counselling burden.

PMID: 29961766 [PubMed - as supplied by publisher]

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes.

Am J Hum Genet. 2018 Jun 20;:

Authors: Son JH, Xie G, Yuan C, Ena L, Li Z, Goldstein A, Huang L, Wang L, Shen F, Liu H, Mehl K, Groopman EE, Marasa M, Kiryluk K, Gharavi AG, Chung WK, Hripcsak G, Friedman C, Weng C, Wang K

Abstract
Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.

PMID: 29961570 [PubMed - as supplied by publisher]