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.

Impact of outpatient non-myeloablative haematopoietic stem cell transplantation in quality of life vs. conventional therapy.

The role of outpatient hematopoietic stem cell transplantation (HSCT) as a therapeutic tool has been strengthened significantly because of the increasing number of patients undergoing this treatment. Due the very nature of this procedure, one of the aspects that should not be overlooked is the quality of life (QOL) of patients undergoing HSCT. Thus, one must consider not only health status after treatment, but also, the psychosocial implications for the patient. This is an observational, longitudinal, and prospective study to assess QOL in patients undergoing outpatient HSCT vs. similar patients receiving medical treatment (MxTx). By applying the COOP/WONKA charts on five occasions (pre-HSCT/initial, post-HSCT/first month, and at 3, 6, and 9 months), thirty-eight patients were analysed, 19 with HSCT and 19 with MxTx with no differences in age, gender or diagnosis. The initial survey found significant differences only in pain perception, which was higher in the HSCT group (p = .08); at the first month, there was a greater tendency for feelings of depression or anxiety in the HSCT group (p = .016), with more limitations in social (p = .003) and daily (p = .044) activities. From 3 months post-HSCT, the results were very similar. The differences persisted only in the area of social activities. Four patients developed graft-versus-host disease with no significant difference in the scores obtained compared to other transplant patients at 3, 6, and 9 months (p = .26) of follow-up.

Low incidence and severity of graft-versus-host disease after outpatient allogeneic peripheral blood stem cell transplantation employing a reduced-intensity conditioning.

BACKGROUND: The prevalence and features of graft-versus-host disease (GVHD) in patients receiving allografts using peripheral blood stem cells (PBSCs) after a reduced-intensity conditioning (RIC) regimen are not well known. Several features of GVHD in patients at two institutions using RIC were assessed. METHODS: We analysed the overall survival (OS) and prevalence of GVHD in patients who underwent outpatient allogeneic PBSC transplantation after RIC between October 1998 and July 2008. RESULTS: We included 301 patients with a median age of 30 yrs (range, 1-71 yrs). In 37 cases, allogeneic peripheral blood stem cell transplantation was indicated for non-malignant disease, and in 264 for malignant disease. The median OS was 35 months. The estimated 3-yr OS was 48%. A total of 154 patients developed GVHD: there were 64 acute, 50 chronic and 40 cases that progressed from acute to chronic. Of the 104 patients with acute GVHD (aGVHD), 40% had grade I and 60% had grades II-IV. Of the 90 patients with chronic GVHD (cGVHD), 67% had limited and 33% had extensive forms. A total of 160 patients died, 40 as a result of GVHD (24 from aGVHD and 16 from cGVHD), 50 as a result of progressive disease and 70 from diverse causes. CONCLUSIONS: The incidence of GVHD was lower than in other series using conventional myeloablative preparative regimens. Most importantly, the severity of GVHD did not significantly affect the long-term survival.

Telangiectasia hemorrágica hereditaria durante el embarazo: Reporte de caso / Hereditary hemorrhagic telangiectasia during pregnancy: Case report

Resumen ANTECEDENTES: La telangiectasia hemorrágica hereditaria, o síndrome de Rendu-Osler-Weber, es una enfermedad vascular, hereditaria y autosómica caracterizada por telangiectasias mucocutáneas y malformaciones arteriovenosas en el pulmón, el cerebro e hígado. La prevalencia estimada es de 1.5 a 2 personas afectadas por cada 10,000 habitantes. El 90% de los casos se debe a una mutación en el gen endoglina y en el de la cinasa 1 similar al receptor de activina (ACVRL1). En la mujer embarazada, la telangiectasia hemorrágica hereditaria es de alto riesgo, sobre todo durante el segundo y tercer trimestre. OBJETIVO: Reportar un caso de telangiectasia hemorrágica hereditaria y exponer las complicaciones que pueden registrarse durante el embarazo. CASO CLÍNICO: Paciente de 23 años, con antecedente heredofamiliar de madre con diagnóstico de telangiectasia hemorrágica hereditaria (síndrome de Osler-Weber-Rendu) que falleció a los 38 años. Antecedente personal patológico de telangiectasia hemorrágica hereditaria, con diagnóstico a los 12 años luego de múltiples episodios de epistaxis. Recibió tratamiento con transfusiones sanguíneas en múltiples ocasiones y 200 mg de sulfato ferroso cada 24 horas. CONCLUSIÓN: La telangiectasia hemorrágica hereditaria condiciona, en la mujer embarazada, la aparición de complicaciones que pueden poner en riesgo la vida de la madre y el feto. Las mujeres con antecedente conocido deben valorarse antes de la concepción con el propósito de conocer el estado de la enfermedad.

Abstract BACKGROUND: Hereditary hemorrhagic telangiectasia, or Rendu-Osler-Weber syndrome, is an autosomal inherited vascular disease characterized by mucocutaneous telangiectasias and arteriovenous malformations in the lung, brain and liver. The estimated prevalence is 1.5 to 2 affected persons per 10,000 population. Ninety percent of cases are due to a mutation in the endoglin gene and in the activin receptor-like kinase 1 gene (ACVRL1). In pregnant women, hereditary hemorrhagic telangiectasia is high risk, especially during the second and third trimester. OBJECTIVE: To report a case of hereditary hemorrhagic telangiectasia and to expose the complications that can occur during pregnancy. CLINICAL CASE: 23-year-old patient, with hereditary family history of mother diagnosed with hereditary hemorrhagic telangiectasia (Osler-Weber-Rendu syndrome) who died at 38 years of age. Personal pathological history of hereditary hemorrhagic telangiectasia, diagnosed at the age of 12 years after multiple episodes of epistaxis. She was treated with multiple blood transfusions and 200 mg of ferrous sulfate every 24 hours. CONCLUSION: Hereditary hemorrhagic telangiectasia conditions, in pregnant women, the appearance of complications that can put the life of the mother and fetus at risk. Women with a known history should be evaluated before conception in order to know the status of the disease.

Comparative analysis of iron status and other hematological parameters in preeclampsia.

OBJECTIVE: To compare serum ferritin (SF) concentrations and other hematological parameters between patients with preeclampsia (PE) and normal pregnant women of the same gestational period who received supplemental iron during pregnancy. METHODS: Prospective, comparative, observational pilot study that included 31 women with PE and 30 healthy pregnant women, at 20 weeks' of gestation. Ferritin, iron and complete blood cell count were compared between groups. RESULTS: In comparison with controls, preeclamptic patients had a higher weight, body mass index, and arterial pressure. Serum ferritin and serum iron were higher in patients with PE (median: 36.5 µg/l vs. 20.9 µg/l and 103.9 µg/dl vs. 90.8 µg/dl) with a significant difference (P = 0.019 and P = 0.345). SF values >40 µg/l correlated with PE (r = 0.281; P = 0.032). A platelet count less than 100 × 109/l was higher in the PE group than in the control group (13% vs. 3%, P = 0.354). CONCLUSION: Higher SF levels, despite being within normal range, were associated with PE. The incidence of thrombocytopenia was higher in preeclamptic women, however, the remaining hematological parameters were similar in both groups.

Endometriosis polipoide: una variante de la endometriosis / Polypoid endometriosis: A variant of endometriosis

Resumen: ANTECEDENTES: La endometriosis polipoide describe una variante poco común de la endometriosis, con características histológicas que simulan un pólipo endometrial y posibilidad de transformación maligna. CASO CLÍNICO: Paciente de 46 años, acudió a consulta por dolor abdominal y sangrado uterino anormal. Los estudios de imagen revelaron una masa heterogénea de forma irregular, adyacente al ovario. Los análisis de sangre reportaron concentraciones elevadas de Ca-125 (75.2 U/mL). El tratamiento consistió en resección quirúrgica mediante laparotomía. El reporte de histopatología fue: endometriosis polipoide. Actualmente la paciente permanece en vigilancia médica, sin recidiva de la enfermedad. CONCLUSIONES: La endometriosis polipoide es una variante poco común de la endometriosis, con posibilidad de evolución maligna. Es importante conocer la enfermedad, con la finalidad de ofrecer el tratamiento adecuado.

Abstract: BACKGROUND: Polypoid endometriosis was first introduced in 1980. It was used to describe an uncommon variant of endometriosis with histological features simulating an endometrial polyp and may be at risk of malignant transformation. CLINICAL CASE: A 46-year-old female presented with lower abdominal pain and Abnormal uterine bleeding. Image studies revealed an irregular shaped, heterogeneous mass adjacent to the ovary. Blood tests showed an elevated CA-125 value (75.2 U/ml). Resection of the mass was performed by laparotomy and the definitive study of histopathology revealed polypoid endometriosis. Currently the patient continues in surveillance without disease recurrence. CONCLUSIONS: Polypoid endometriosis is an uncommon variant of endometriosis, with the possibility of malignant evolution. This rare form of disease should be known, in order to provide adequate treatment for the patient.

Tratamiento y desenlace obstétrico de una paciente con artrogriposis múltiple congénita / Clinical treatment and outcome of a patient with arthrogryposis multiplex congenita

Resumen ANTECEDENTES: La artrogriposis múltiple congénita es una alteración excepcional, caracterizada por contracturas musculares en diversas partes del cuerpo. Las pacientes embarazadas con esta enfermedad tienen mayor riesgo de complicaciones obstétricas. CASO CLÍNICO: Paciente de 19 años, con artrogriposis múltiple congénita, de ocho semanas de embarazo, quien acudió al servició médico para iniciar el control prenatal. Recibió asesoría de los riesgos cardiovasculares y del sistema respiratorio, secundarios a la enfermedad de base, que pudieran exacerbarse por el embarazo. El ultrasonido efectuado en la semana 22 del embarazo no reportó alteraciones estructurales. La paciente continuó en control prenatal, sin dificultad respiratoria ni alteraciones cardiovasculares. No recibió anticoagulantes profilácticos, ni manifestó signos de trombosis durante el embarazo. Se decidió la interrupción del embarazo por cesárea, debido a la limitación del movimiento de la cadera. Se programó para cirugía en la semana 38.3 del embarazo, con valoración del servicio de Cardiología, quienes reportaron fracción de eyección del ventrículo izquierdo adecuada y sin evidencia de miocardiopatía. Se aplicó anestesia por vía epidural sin complicaciones. El examen físico del neonato no mostró alteraciones. Actualmente, la madre y su hijo permanecen con buen estado de salud. CONCLUSIONES: Las pacientes embarazadas con artrogriposis múltiple congénita deben recibir asesoría de los riesgos inherentes y posibles complicaciones de la enfermedad. Es importante la intervención de un equipo multidisciplinario, para evaluar la función cardiovascular y respiratoria, además de efectuar revisiones seriadas para asegurar el bienestar materno-fetal.

Abstract BACKGROUND: Arthrogryposis multiplex congenita is a rare entity characterized by the appearance of multiple muscle contractures in various parts of the body. Pregnant patients with this condition have a higher risk of complications in obstetric management. CLINICAL CASE: A 19-year-old patient, with arthrogryposis multiplex congenita, eight weeks pregnant, attended in medical service to start prenatal care. Received advice on the cardiovascular and respiratory system risks, secondary to the underlying disease, that could be exacerbated by pregnancy. The ultrasound during the 22nd week of pregnancy did not report any structural alterations. The patient continued in prenatal control, without respiratory difficulty or cardiovascular alterations. Did not receive prophylactic anticoagulants, neither showed signs of thrombosis. We decide finished the pregnancy by caesarean section, due to the limited movement of the hip. Surgery was scheduled at week 38.3 of pregnancy, with assessment by the Cardiology service, who reported adequate left ventricular ejection fraction and no evidence of cardiomyopathy. Epidural anesthesia was applied without complications. The physical examination of the newborn showed no alterations. Currently, the mother and her son remain in good health. CONCLUSIONS: In pregnant patients with arthrogryposis multiplex congenita its important to explain the inherent risks of their condition and their possible complications. Multidisciplinary management should be performed with cardiovascular, respiratory, and serial reviews to ensure the welfare of the maternal-fetal binomial.

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI.

BACKGROUND: Identification of bona fide direct nuclear receptor gene targets has been challenging but essential for understanding regulation of organismal physiological processes. RESULTS: We describe a methodology to identify transcription factor binding sites and target genes in vivo by intersecting microarray data, computational binding site queries, and evolutionary conservation. We provide detailed experimental validation of each step and, as a proof of principle, utilize the methodology to identify novel direct targets of the orphan nuclear receptor NR2F1 (COUP-TFI). The first step involved validation of microarray gene expression profiles obtained from wild-type and COUP-TFI(-/-) inner ear tissues. Secondly, we developed a bioinformatic tool to search for COUP-TFI DNA binding sites in genomes, using a classification-type Hidden Markov Model trained with 49 published COUP-TF response elements. We next obtained a ranked list of candidate in vivo direct COUP-TFI targets by integrating the microarray and bioinformatics analyses according to the degree of binding site evolutionary conservation and microarray statistical significance. Lastly, as proof-of-concept, 5 specific genes were validated for direct regulation. For example, the fatty acid binding protein 7 (Fabp7) gene is a direct COUP-TFI target in vivo because: i) we identified 2 conserved COUP-TFI binding sites in the Fabp7 promoter; ii) Fapb7 transcript and protein levels are significantly reduced in COUP-TFI(-/-) tissues and in MEFs; iii) chromatin immunoprecipitation demonstrates that COUP-TFI is recruited to the Fabp7 promoter in vitro and in vivo and iv) it is associated with active chromatin having increased H3K9 acetylation and enrichment for CBP and SRC-1 binding in the newborn brain. CONCLUSION: We have developed and validated a methodology to identify in vivo direct nuclear receptor target genes. This bioinformatics tool can be modified to scan for response elements of transcription factors, cis-regulatory modules, or any flexible DNA pattern.