Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection.

The cattle reference genome assembly has underpinned major innovations in beef and dairy genetics through genome-enabled selection, including removal of deleterious recessive variants and selection for favorable alleles affecting quantitative production traits. The initial reference assemblies, up to and including UMD3.1 and Btau4.1, were based on a combination of clone-by-clone sequencing of bacterial artificial chromosome clones generated from blood DNA of a Hereford bull and whole-genome shotgun sequencing of blood DNA from his inbred daughter/granddaughter named L1 Dominette 01449 (Dominette). The approach introduced assembly gaps, misassemblies, and errors, and it limited the ability to assemble regions that undergo rearrangement in blood cells, such as immune gene clusters. Nonetheless, the reference supported the creation of genotyping tools and provided a basis for many studies of gene expression. Recently, long-read sequencing technologies have emerged that facilitated a re-assembly of the reference genome, using lung tissue from Dominette to resolve many of the problems and providing a bridge to place historical studies in common context. The new reference, ARS-UCD1.2, successfully assembled germline immune gene clusters and improved overall continuity (i.e., reduction of gaps and inversions) by over 250-fold. This reference properly places nearly all of the legacy genetic markers used for over a decade in the industry. In this review, we discuss the improvements made to the cattle reference; remaining issues present in the assembly; tools developed to support genome-based studies in beef and dairy cattle; and the emergence of newer genome assembly methods that are producing even higher-quality assemblies for other breeds of cattle at a fraction of the cost. The new frontier for cattle genomics research will likely include a transition from the individual Hereford reference genome, to a "pan-genome" reference, representing all the DNA segments existing in commonly used cattle breeds, bringing the cattle reference into line with the current direction of human genome research.

Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2.

In cattle, the X chromosome accounts for approximately 3 and 6% of the genome in bulls and cows, respectively. In spite of the large size of this chromosome, very few studies report analysis of the X chromosome in genome-wide association studies and genomic selection. This lack of genetic interrogation is likely due to the complexities of undertaking these studies given the hemizygous state of some, but not all, of the X chromosome in males. The first step in facilitating analysis of this gene-rich chromosome is to accurately identify coordinates for the pseudoautosomal boundary (PAB) to split the chromosome into a region that may be treated as autosomal sequence (pseudoautosomal region) and a region that requires more complex statistical models. With the recent release of ARS-UCD1.2, a more complete and accurate assembly of the cattle genome than was previously available, it is timely to fine map the PAB for the first time. Here we report the use of SNP chip genotypes, short-read sequences, and long-read sequences to fine map the PAB (X chromosome:133,300,518) and simultaneously determine the neighboring regions of reduced homology and true pseudoautosomal region. These results greatly facilitate the inclusion of the X chromosome in genome-wide association studies, genomic selection, and other genetic analysis undertaken on this reference genome.

Non-invasive half millimetre 32 detector row computed tomography angiography accurately excludes significant stenoses in patients with advanced coronary artery disease and high calcium scores.

OBJECTIVE: To show an overall diagnostic accuracy > or = 90% for detection of > or = 50% stenoses by coronary half millimetre 32 detector row computed tomography angiography (32 x 0.5-MDCTA) in patients with advanced coronary artery disease (CAD) and a high likelihood of raised calcium scores. METHODS: ECG gated 32 x 0.5-MDCTA (32 x 0.5 mm cross sections, 0.35 x 0.35 x 0.35 mm3 isotropic voxels, 400 ms rotation) was performed after injection of iodixanol (120 ml, 320 mg/ml) in 30 consecutive patients (25 men, mean (SD) age 59 (13) years, body mass index 26.2 (4.9) kg/m2). Native arteries, including > or = 1.5 mm branches, and bypass grafts were screened for > or = 50% stenoses. Stents were excluded. Conventional coronary angiography (performed 18 (12) days before 32 x 0.5-MDCTA) was analysed by quantitative coronary angiography. RESULTS: Median Agatston calcium score was 510 (range 3-5066). Sensitivity, specificity, and positive and negative predictive values for detection of > or = 50% stenoses in native arteries were 76% (29 of 38), 94% (190 of 202), 71% (29 of 41), and 96% (190 of 199), respectively. Overall diagnostic accuracy was 91% (219 of 240). Due to the following artefacts 20% (69 of 352) of the vessels were excluded: motion, noise, and low contrast enhancement isolated or in combination (45 of 69 (65%)); image distortion by implantable cardioverter-defibrillator or pacemaker leads (18 of 69 (26%)); and blooming secondary to severe calcification (6 of 69 (9%)). CONCLUSIONS: Coronary 32 x 0.5-MDCTA accurately excludes > or = 50% stenoses in patients with advanced CAD and high calcium scores with an overall diagnostic accuracy of 91%.

Carotid body tumor: diagnostic and therapeutic approach.

Carotid body tumor may be clinically suspected when the only clues are physiologic manifestations of carotid body dysfunction or when a palpable cervical mass is evident upon presentation. In the latter case, the physiologic signs of carotid body dysfunction are usually recognizable. We have presented the case of a patient who was completely disabled by a slowly enlarging carotid body tumor. An attempt at surgical excision of the tumor was unsuccessful because of its proximity and adhesion to vital neck structures. An endocardial pacemaker inserted to ameliorate the episodes of bradycardia and hypotension accompanied by transient complete atrioventricular block resulted in only partial and temporary relief. Finally, irradiation of the tumor induced fast shrinkage and rapid regression of symptoms.

Effects of chronic cyclosporine administration on renal blood flow and intrarenal blood flow distribution.

Cyclosporine-induced decreases in renal blood flow (RBF) and glomerular function are well documented. Glomerular filtration and tubular function may be affected by changes in both total renal blood flow and cortical blood flow distribution (CBFD). The effect of CsA on RBF, CBFD, glomerular filtration rate, and tubular function was studied in conscious ewes receiving a mean CsA dose of 30 mg/kg/day for 28 days with mean CsA trough levels of 344 +/- 45 ng/ml. RBF and CBFD were determined by the injection of 15 microns radioactive microspheres before and after one month of treatment with CsA or its vehicle, olive oil. RBF decreased by 24% from 7.65 +/- 0.87 to 5.79 +/- 0.42 ml/min/g of kidney in CsA-treated ewes (P = 0.014), while no decrease was noted in the control group (7.92 +/- 1.10 vs. 7.62 +/- 0.71). Intracortical blood flow decreased in proportion to the fall in total renal blood flow--thus CsA treatment did not change the cortical distribution of flow. There was a 25% decrease in GFR, as determined by inulin clearance, in the CsA-treated group (80 +/- 6 vs. 62 +/- 3 ml/min; P = 0.027) while there was a nonsignificant increase in control animals (62 +/- 11 vs. 92 +/- 7 ml/min). There was no evidence of tubular dysfunction in either group. There were also no changes in urinary excretion rates of prostaglandins PGE2, 6-keto-PGF1 alpha or thromboxane B2, nor were there changes in plasma renin activity. CsA induced decreases in RBF occur red without redistribution of cortical blood flow, indicating that altered cortical distribution of blood flow is not responsible for the changes in GFR or tubular function that have been reported. The changes in renal blood flow and glomerular filtration rate are independent of changes in renal prostaglandin production, and are likely not associated with altered plasma renin activity.