scholarly journals Haplotype-resolved germline and somatic alterations in renal medullary carcinomas

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Kar-Tong Tan ◽  
Hyunji Kim ◽  
Jian Carrot-Zhang ◽  
Yuxiang Zhang ◽  
Won Jun Kim ◽  
...  

Abstract Background Renal medullary carcinomas (RMCs) are rare kidney cancers that occur in adolescents and young adults of African ancestry. Although RMC is associated with the sickle cell trait and somatic loss of the tumor suppressor, SMARCB1, the ancestral origins of RMC remain unknown. Further, characterization of structural variants (SVs) involving SMARCB1 in RMC remains limited. Methods We used linked-read genome sequencing to reconstruct germline and somatic haplotypes in 15 unrelated patients with RMC registered on the Children’s Oncology Group (COG) AREN03B2 study between 2006 and 2017 or from our prior study. We performed fine-mapping of the HBB locus and assessed the germline for cancer predisposition genes. Subsequently, we assessed the tumor samples for mutations outside of SMARCB1 and integrated RNA sequencing to interrogate the structural variants at the SMARCB1 locus. Results We find that the haplotype of the sickle cell mutation in patients with RMC originated from three geographical regions in Africa. In addition, fine-mapping of the HBB locus identified the sickle cell mutation as the sole candidate variant. We further identify that the SMARCB1 structural variants are characterized by blunt or 1-bp homology events. Conclusions Our findings suggest that RMC does not arise from a single founder population and that the HbS allele is a strong candidate germline allele which confers risk for RMC. Furthermore, we find that the SVs that disrupt SMARCB1 function are likely repaired by non-homologous end-joining. These findings highlight how haplotype-based analyses using linked-read genome sequencing can be applied to identify potential risk variants in small and rare disease cohorts and provide nucleotide resolution to structural variants.

Author(s):  
Rachel K.Y. Hung ◽  
Elizabeth Binns-Roemer ◽  
John W. Booth ◽  
Rachel Hilton ◽  
Julie Fox ◽  
...  

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4920-4920
Author(s):  
Hyacinth Idu Hyacinth ◽  
Cara Carty ◽  
Gregory L. Burke ◽  
Rakhi P. Naik ◽  
Robert J. Adams ◽  
...  

Abstract Background African Americans experience higher rates of cardiovascular disease (CVD) and mortality from stroke and coronary heart disease. It is possible that genetic modifiers associated with African ancestry may confer higher risk of CVD. The sickle cell mutation results from a functional single nucleotide polymorphism (SNP) involving the substitution of GTG (valine) for a GAG (glutamic acid) in the gene encoding beta globin. Heterozygosity for the mutation (rs334) results in sickle cell trait (SCT) which is prevalent among 8% of African Americans, while homozygosity produces sickle cell anemia. Sickle cell trait has been deemed clinically benign yet recent evidence shows that it is associated with increased risk of chronic kidney disease, a 2 times increased risk for venous thromboembolism and a 4 times increased risk for pulmonary embolism. Further, there is evidence that individuals with SCT have higher serum levels of C-reactive protein, Fibrinogen 2.1 fragments and D-dimers. We hypothesized that African Americans with SCT have a higher risk for cardiovascular outcomes than those without SCT (homozygous wild-type hemoglobin). Methods Data were obtained from the Multi-Ethnic Study of Atherosclerosis (MESA), Jackson Heart Study (JHS) and Women’s Health Initiative (WHI). Incident myocardial infarction (MI) was defined as adjudicated non-fatal or fatal MI, coronary heart disease (CHD) was defined as a composite endpoint including adjudicated non-fatal MI, fatal CHD, or documented coronary revascularization procedure. Sickle cell trait was identified either by direct genotyping or imputation for rs334. Individuals who were homozygous for the sickle mutation or had a prior history of CHD events were excluded. Cox proportional hazards models were used to estimate a hazard ratio (HR) of incident MI or CHD comparing sickle cell trait carriers to non-carriers. Models were adjusted for age, sex and principal component of global ancestry. Analysis was performed separately in each cohort and the results were subsequently meta-analyzed using a fixed effect inverse variance weighted method. Results A total of 11,128 African American men and women were included in the pooled data base. The average age at baseline were 62.2 ± 10.1, 49.8 ± 11.8 and 61.4 ± 7.0 years for MESA, JHS and WHI respectively, with JHS participants significantly younger than the other two cohorts (p <0.001). Unlike the MESA and JHS cohorts that included both genders, the WHI cohort was exclusively female. Additionally, the percentage African ancestry was significantly higher among those with SCT compared to those without SCT (82 ± 12% vs. 78 ± 14% for MESA, 84 ± 6% vs. 82 ± 9% for JHS and 79 ± 12% vs. 76 ± 15% for WHI), further the percentage African ancestry was significantly lower among WHI subjects irrespective of carrier status, p <0.01. There was no significant difference between cohorts in the prevalence of diabetes or hypertension, mean blood pressure levels, or proportion of smokers (table 1). The HR for incident MI was 1.56 (0.66 – 3.68) in MESA, 1.04 (0.32 – 3.39) in JHS and 0.97 (0.68 – 1.39) in WHI, but was not statistically significant. Further, the HR for incident CHD was 2.73 (1.52 – 4.89) in MESA, 1.14 (0.46 – 2.89) in JHS and 0.97 (0.68 – 1.17) in WHI, although the HR only achieved statistical significance in MESA (p<0.001). Overall, sickle cell trait was not significantly associated with incident MI (1.04 [0.76 – 1.43]) or CHD (1.11 [0.85 – 1.43] figure 1). Limitation/Recommendations and Conclusion The overall result from this study did not demonstrate a significant association between SCT and CHD. This may reflect inadequate power due to the relatively small number of CHD events and differences in study design. This study suggests the need for a well powered study to test this hypothesis, the result of which could have significant impact on the approach to risk factor modification for African Americans. Figure 1 Figure 1. Figure 2 Figure 2. Disclosures Naik: NHLBI: Research Funding.


1977 ◽  
Vol 137 (3) ◽  
pp. 281a-281
Author(s):  
P. E. Mickelson

2020 ◽  
pp. 1-2
Author(s):  
Michael Alperovich ◽  
Eric Park ◽  
Michael Alperovich ◽  
Omar Allam ◽  
Paul Abraham

Although sickle cell disease has long been viewed as a contraindication to free flap transfer, little data exist evaluating complications of microsurgical procedures in the sickle cell trait patient. Reported is the case of a 55-year-old woman with sickle cell trait who underwent a deep inferior epigastric perforator (DIEP) microvascular free flap following mastectomy. The flap developed signs of venous congestion on postoperative day two but was found to have patent arterial and venous anastomoses upon exploration in the operating room. On near-infrared indocyanine green angiography, poor vascular flow was noted despite patent anastomoses and strong cutaneous arterial Doppler signals. Intrinsic microvascular compromise or sickling remains a risk in the sickle cell trait population as it does for the sickle cell disease population. Just like in sickle cell disease patients, special care should be taken to optimize anticoagulation and minimize ischemia-induced sickling for patients with sickle cell trait undergoing microsurgery.


2020 ◽  
Author(s):  
Ayo Priscille Doumatey ◽  
Hermon Feron ◽  
Kenneth Ekoru ◽  
Jie Zhou ◽  
Adebowale Adeyemo ◽  
...  

2021 ◽  
pp. 100047
Author(s):  
Álvaro Alejandre-de-Oña ◽  
Jaime Alonso-Muñoz ◽  
Pablo Demelo-Rodríguez ◽  
Jorge del-Toro-Cervera ◽  
Francisco Galeano-Valle

Blood ◽  
1963 ◽  
Vol 22 (3) ◽  
pp. 334-341 ◽  
Author(s):  
RICHARD D. LEVERE ◽  
HERBERT C. LICHTMAN ◽  
Joan Levine

Abstract The relative rates of incorporation of Fe59 into heterogenic hemoglobins was studied in four patients with sickle cell trait. Three of the patients were free of superimposed disease, while one had active pulmonary tuberculosis. In all subjects there was a significantly greater incorporation of radioiron, per milligram of hemoglobin, into hemoglobin S than into hemoglobin A. The data indicate that in sickle cell trait the rates of synthesis of the heterogenic hemoglobins are not proportional to their circulating concentrations. Two interpretations appear possible. Since the size of the intra-marrow pool of hemoglobin S was not known, it is possible that there exists a smaller preformed pool of the abnormal hemoglobin, with the isotope making its appearance first in hemoglobin S. However, it is also possible that hemoglobin S is synthesized at a rate which is greater than that reflected by its circulating concentration. This implies that the relative concentrations of hemoglobin S and hemoglobin A vary from erythrocyte to erythrocyte, and that those cells with the greatest proportion of hemoglobin S are selectively destroyed.


1975 ◽  
Vol 250 (22) ◽  
pp. 8630-8634 ◽  
Author(s):  
JR Shaeffer ◽  
MA Longley ◽  
J DeSimone ◽  
LJ Kleve

2012 ◽  
Vol 22 (3) ◽  
pp. 331-333
Author(s):  
C. Désidéri-Vaillant ◽  
J. Sapin-Lory ◽  
L. Di Costanzo ◽  
C. Cano ◽  
D. Lambrechts ◽  
...  

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