Genomic analyses of tropical beef cattle fertility based on genotyping pools of Brahman cows with unknown pedigree

We introduce an innovative approach to lowering the overall cost of obtaining genomic EBV (GEBV) and encourage their use in commercial extensive herds of Brahman beef cattle. In our approach, the DNA genotyping of cow herds from 2 independent properties was performed using a high-density bovine SNP chip on DNA from pooled blood samples, grouped according to the result of a pregnancy test following their first and second joining opportunities. For the DNA pooling strategy, 15 to 28 blood samples from the same phenotype and contemporary group were allocated to pools. Across the 2 properties, a total of 183 pools were created representing 4,164 cows. In addition, blood samples from 309 bulls from the same properties were also taken. After genotyping and quality control, 74,584 remaining SNP were used for analyses. Pools and individual DNA samples were related by means of a "hybrid" genomic relationship matrix. The pooled genotyping analysis of 2 large and independent commercial populations of tropical beef cattle was able to recover significant and plausible associations between SNP and pregnancy test outcome. We discuss 24 SNP with significant association ( < 1.0 × 10) and mapped within 40 kb of an annotated gene. We have established a method to estimate the GEBV in young herd bulls for a trait that is currently unable to be predicted at all. In summary, our novel approach allowed us to conduct genomic analyses of fertility in 2 large commercial Brahman herds managed under extensive pastoral conditions.

Using CRP to predict anastomotic leakage after open and laparoscopic colorectal surgery: is there a difference?

AIM

C-reactive protein (CRP) has proven to be a useful adjunct in early diagnosis of anastomotic leak (AL) after colorectal surgery. It would be of considerable value to examine whether modality of surgery has influence upon postoperative CRP serum levels and their predictive value in the diagnosis of AL.

METHODS

All patients undergoing elective colorectal surgery with anastomosis were enrolled into a prospective database between 2011 and 2014. AL was defined with strict operative and radiological criteria. Outcomes between open and laparoscopic resections were assessed statistically and Receiver Operating Characteristic (ROC) curve analysis performed.

RESULTS

Seven hundred twenty-seven patients with an intestinal anastomosis were identified including 468 laparoscopic procedures (468/727; 64 %). There were 58 anastomotic leaks (58/727; 7.9 %) of which 29 (6.2 %) were laparoscopic and 29 (11.2 %) were open. Mean CRP levels were significantly higher in patients after open surgery compared with laparoscopic both with AL (p = 0.013), and without (p = 0.02). ROC curve analysis revealed postoperative day 3 (cut-off CRP 209) and day 4 (cut-off CRP 123.5) to be most predictive of leak in the open group with an area under the curve (AUC) 0.794 (sensitivity 80 %, specificity 80 %) and AUC 0.806 (sensitivity 94 %, specificity 60 %), respectively. In the laparoscopic group, day 2 proved to be the most accurate day for detection of leak with a cut-off CRP of 146.5 showing 75 % sensitivity and a 70 % specificity (AUC 0.766).

CONCLUSION

CRP levels are higher after open surgery compared with laparoscopic surgery, both with and without AL. AL generates a significant detectable increase in CRP within 2-4 days after surgery.

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.

Lessons learnt in the management of primary invasive penile cancer in an Australian tertiary referral centre: clinical outcomes with a minimum 48 months follow-up study

Purpose

To report on lessons learnt in the management of primary invasive penile cancer in a major tertiary hospital in Australia.

Materials and Methods

Medical records for all patients who underwent surgery for primary invasive penile cancer between January 2000 and January 2011 were obtained. Patient demographics, clinical status of inguinal node, cancer stage and clinical outcomes were reviewed. All patients were followed up for a minimum of 48 months postoperative unless patient deceased within the first 48 months from the time of penile cancer surgery.

Results

Over the 11-year period, a total of 23 cases of invasive penile cancer were identified. Partial penectomy was the most common form of organ preserving surgery and the majority of patients have pT1b disease. Of the 9 patients with clinically palpable inguinal nodes, 7 patients were diagnosed with pN3 disease following inguinal lymphadenectomy. The Kaplan-Meier cancer-specific survival at 72 months showed decreasing survival based on tumour stage (83% in pT1, 79% in pT2, and 64% in pT3 disease) and nodal disease (100% in node negative, 50% in superficial inguinal lymphadenopathy, and 38% in patients with deep inguinal and/or pelvic lymphadenopathy) (p=0.082). The Kaplan-Meier cancer-specific survival revealed statistically significant difference in survival outcome in patients with local recurrence vs. systemic metastasis disease (33% vs. 17%, p=0.008).

Conclusions

The presence of high risk features such as tumour stage, lymph node involvement and distant metastasis carries a significant higher risk of death and tumour recurrence in patients with penile cancer and inguinal lymph node metastasis.

Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution

BACKGROUND

Genomic analysis of multi-focal renal cell carcinomas from an individual with a germline VHL mutation offers a unique opportunity to study tumor evolution.

RESULTS

We perform whole exome sequencing on four clear cell renal cell carcinomas removed from both kidneys of a patient with a germline VHL mutation. We report that tumors arising in this context are clonally independent and harbour distinct secondary events exemplified by loss of chromosome 3p, despite an identical genetic background and tissue microenvironment. We propose that divergent mutational and copy number anomalies are contingent upon the nature of 3p loss of heterozygosity occurring early in tumorigenesis. However, despite distinct 3p events, genomic, proteomic and immunohistochemical analyses reveal evidence for convergence upon the PI3K-AKT-mTOR signaling pathway. Four germline tumors in this young patient, and in a second, older patient with VHL syndrome demonstrate minimal intra-tumor heterogeneity and mutational burden, and evaluable tumors appear to follow a linear evolutionary route, compared to tumors from patients with sporadic clear cell renal cell carcinoma.

CONCLUSIONS

In tumors developing from a germline VHL mutation, the evolutionary principles of contingency and convergence in tumor development are complementary. In this small set of patients with early stage VHL-associated tumors, there is reduced mutation burden and limited evidence of intra-tumor heterogeneity.

Do we need a different organ allocation system for kidney transplants using donors after circulatory death?

BACKGROUND

There is no national policy for allocation of kidneys from Donation after circulatory death (DCD) donors in the UK. Allocation is geographical and based on individual/regional centre policies. We have evaluated the short term outcomes of paired kidneys from DCD donors subject to this allocation policy.

METHODS

Retrospective analysis of paired renal transplants from DCD's from 2002 to 2010 in London. Cold ischemia time (CIT), recipient risk factors, delayed graft function (DGF), 3 and 12 month creatinine) were compared.

RESULTS

Complete data was available on 129 paired kidneys.115 pairs were transplanted in the same centre and 14 pairs transplanted in different centres. There was a significant increase in CIT in kidneys transplanted second when both kidneys were accepted by the same centre (15.5 ± 4.1 vs 20.5 ± 5.8 hrs p<0.0001 and at different centres (15.8 ± 5.3 vs. 25.2 ± 5.5 hrs p=0.0008). DGF rates were increased in the second implant following sequential transplantation (p=0.05).

CONCLUSIONS

Paired study sequential transplantation of kidneys from DCD donors results in a significant increase in CIT for the second kidney, with an increased risk of DGF. Sequential transplantation from a DCD donor should be avoided either by the availability of resources to undertake simultaneous procedures or the allocation of kidneys to 2 separate centres.

Patients' perceptions of surgical registrars' training in the private hospital setting

What's known on the subject? and What does the study add? The Australian private health sector is increasingly being recognised as an opportunity for advanced surgical training. Little is known about what the patients think of urology training in the private sector. Patients perceptions on the place of urology registrars in the Australian private sector are assessed for the first time. We can confirm that there appears to be acceptance of urology training in the private sector.

OBJECTIVE

• To determine the acceptance of surgical trainees in a private hospital setting.

METHOD

• This was an ethics approved prospective study using a written survey. • A total of 177 consecutive patients presenting for private consultation were recruited. A self-administered written survey was completed by each patient in the waiting room prior to consultation.

RESULTS

• Only 36.8% of subjects (confidence interval 29.6-44.1) initially understood the term registrar which significantly increased to 75% (confidence interval 68.4-81.6, P < 0.05) after reading explanatory notes. • Perceived differences between private and public hospitals were choice of surgeon (28%), waiting times for an operation (28%), standard of care (17%), cost (16%) and waiting times for an appointment (11%). • Patients' acceptance of registrar involvement with either a small part of an operation, a large part of an operation, the whole operation and assistance only were 34%, 16%, 13% and 37%.

CONCLUSIONS

• Patients have a poor understanding of the term registrar. • Acceptance of registrars in private hospitals is increased if consultant involvement is emphasized. • Surgical assistance and performance of minor parts of surgery by trainees is well accepted.