AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap.

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen's alleles and none from the many drones she mated with. Thus the ordered combination or 'phase' of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.

Optical mapping compendium of structural variants across global cattle breeds.

Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution.

A cattle graph genome incorporating global breed diversity.

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.

Investigating the population structure and genetic differentiation of livestock guard dog breeds.

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

A method for single nucleotide polymorphism selection for parentage assessment in goats.

Accurate pedigrees are essential to optimize genetic improvement and conservation of animal genetic resources. In goats, the use of mating groups and kidding management procedures hamper the identification of parentage. Small panels of single nucleotide polymorphisms (SNP) have been proposed in other species to substitute microsatellites for parentage assessment. Using data from the current GoatSNP50 chip, we developed a new 3-step procedure to identify a low-density SNP panel for highly accurate parentage assessment. Methodologies for SNP selection used in other species are less suitable in the goat because of uncertainties in the genome assembly. The procedure developed in this study is based on parent-offspring identification and on estimation of Mendelian errors, followed by canonical discriminant analysis identification and stepwise regression reduction. Starting from a reference sample of 109 Alpine goats with known pedigree relationships, we first identified a panel of 200 SNP that was further reduced to 2 final panels of 130 and 114 SNP with random coincidental match inclusion of 1.51×10(-57) and 2.94×10(-34), respectively. In our reference data set, all panels correctly identified all parent-offspring combinations, revealing a 40% pedigree error rate in the information provided by breeders. All reference trios were confirmed by official tests based on microsatellites. Panels were also tested on Saanen and Teramana breeds. Although the testing on a larger set of breeds in the reference population is still needed to validate these results, our findings suggest that our procedure could identify SNP panels for accurate parentage assessment in goats or in other species with unreliable marker positioning.

Efficacy and cost-effectiveness of stereotactic vacuum-assisted core biopsy of nonpalpable breast lesions: analysis of 602 biopsies performed over 5 years.

PURPOSE: The authors sought to evaluate the diagnostic accuracy and cost-effectiveness of vacuum-assisted core biopsy (VACB) in comparison with diagnostic surgical excision for characterisation of nonpalpable breast lesions classified as Breast Imaging Reporting and Data System (BI-RADS) categories R3 and R4. MATERIALS AND METHODS: From January 2004 to December 2008, we conducted 602 stereotactic, 11-gauge, VACB procedures on 243 nonpalpable breast lesions categorised as BI-RADS R3, 346 categorised as BI-RADS R4 and 13 categorised as BI-RADS R5. We calculated the diagnostic accuracy and cost savings of VACB by subtracting the cost of the stereotactic biopsy from that of the diagnostic surgical procedure. RESULTS: A total of 56% of the lesions were benign and required no further assessment. Lesions of uncertain malignant potential (B3) (23.6%) were debated at multidisciplinary meetings, and diagnostic surgical biopsy was recommended for 83.1% of them. All malignant lesions (B4 and B5) underwent surgical excision. VACB had a sensitivity of 94.9%, specificity of 98.3% and diagnostic accuracy of 97.7%. The cost savings per VACB procedure were 464.00 euro; by obviating 335 surgical biopsies, the overall cost savings was 155,440.00 euro over 5 years. CONCLUSIONS: VACB proved to have high diagnostic accuracy for characterising abnormalities at low to intermediate risk of malignancy and obviated surgical excision in about half of the cases, allowing for considerable cost savings.

[Magnetic resonance imaging of the small intestine and colon in Crohn's disease]. / La Risonanza Magnetica dell'intestino tenue e del colon nel morbo de Crohn.

Three normal volunteers and 20 patients with known Crohn's disease were examined with MRI--at 0.5 Tesla and with a superconductive magnet. Coronal T1-weighted GE images were mainly acquired, before and after i.v. Gd-DTPA injection in breath hold (TR 70 ms, TE 13 ms, FA 70 degrees). MR findings were compared with the results of small and large bowel enema. In 6 patients (30%) the abnormal loops were missed. In the other 14 patients (70%) MRI did depict the affected loops in the same sites as depicted by conventional radiography. The bowel wall was thickened (4-10 mm) in all patients. In 10 patients the thickened wall was markedly enhanced after Gd-DTPA injection. In 6 patients MRI demonstrated disease complications--i.e., stenoses, fistulae and abscesses--missed by conventional radiography. In 7 patients MRI showed the bowel to be more involved than demonstrated by conventional studies. Bowel wall thickening appeared to be a constant and reliable sign of disease. Wall enhancement was a less frequent sign but, when present, it was considered as characteristic as wall thickening. In the staging of Crohn's disease, MRI yields more pieces of information than conventional radiography and depicts the involvement of the intestinal wall and of its surrounding spaces.

[Post-traumatic hemoperitoneum: role of laparoscopy]. / Emoperitoneo post-traumatico: ruolo della laparoscopia.

The use of laparoscopic as a diagnostic instrument in blunt penetrating abdominal traumas was first proposed by some authors in the 70s. The introduction of sophisticated instrumental tests, such as CAT and echotomography (ETG), confined this method to narrow diagnostic field which was gradually less frequently used. The lively interest expressed by the surgical world and the enormous spread of laparoscopy after the end of the 80s, following the introduction of laparoscopic cholecystectomy, has prompted the renewed use of the laparoscopic technique also in those subjects with blunt abdominal trauma. Over the past 12 months the authors have used laparoscopy in 8 subjects with hemoperitoneum secondary to contusive abdominal trauma in hemodynamically stable conditions, in which instrumental test (CAT and ETG) and peritoneal lavage were positive for the presence of hematic effusion. The use of laparoscopy in 7 patients allowed a wait-and-see approach to be adopted, thus eliminating the need for explorative laparotomy. It was only necessary to proceed with laparotomy in one patient to control bleeding from a major splenic lesion.

[The surgical treatment of perforated colonic diverticulitis]. / Trattamento chirurgico delle diverticoliti perforate del colon.

The authors report a consecutive series of 52 patients who underwent urgent operation because of peritonitis by perforated diverticulitis. Urgent colonic resection achieves the best results.

[An analysis of the surgical risk in elderly subjects with neoplasms of the large intestine. A follow-up of 102 consecutive cases]. / Analisi del rischio operatorio in soggetti anziani affetti da neoplasia del grosso intestino. Controllo di 102 casi consecutivi.

Today surgeons find that they have to operate with increasing frequency on elderly patients suffering from colorectal cancer. This study examined 102 patients with this pathology. The findings show that age alone is not a contraindication for surgery. On the contrary decisive negative factors include both concomitant pathologies and emergency surgery because it is not possible to correct any pre-existing imbalances before surgery. The overall mortality rate is 9% of which 4% after emergency surgery. It is therefore possible to conclude that elderly patients can undergo radical surgery irrespective of age.

[A case of mesenteric panniculitis, resulting in short intestine syndrome after massive surgical resection of the ileum]. / Un caso di panniculite mesenterica, risoltosi in sindrome da intestino corto dopo interventi chirurgici di resezione massiva dell'ileo.

A case of mesenteric panniculitis occurring with recurrent intestinal occlusion is reported. To resolve the serious occlusive condition, a massive intestinal resection had to be carried out, leaving the patient with a short intestine syndrome.

[Congenital deficiency of metahemoglobin-reductases (diaphorases). A case of cyanosis during general anesthesia]. / Deficit congenito di metaemoglobin-reduttasi (diaforasi). Un caso di cianosi in corso di anestesia generale.

A case of cyanosis during general anaesthesia in a patient suffering from congenital deficiency of metahaemoglobin-reductase (diaphorase) is reported. The anaesthesiological technique and the probable triggering cause are analysed. The investigation carried out in members of the family to obtain confirmation of the genetic origin of the enzymatic deficiency is also reported.