Genomic testing for copy number and single nucleotide variants in spermatogenic failure

PURPOSE

To identify clinically significant genomic copy number (CNV) and single nucleotide variants (SNV) in males with unexplained spermatogenic failure (SPGF).

MATERIALS AND METHODS

Peripheral blood DNA from 97/102 study participants diagnosed with oligozoospermia, severe oligozoospermia, or non-obstructive azoospermia (NOA) was analyzed for CNVs via array comparative genomic hybridization (aCGH) and SNVs using whole-exome sequencing (WES).

RESULTS

Of the 2544 CNVs identified in individuals with SPGF, > 90% were small, ranging from 0.6 to 75 kb. Thirty, clinically relevant genomic aberrations, were detected in 28 patients (~ 29%). These included likely diagnostic CNVs in 3/41 NOA patients (~ 7%): 1 hemizygous, intragenic TEX11 deletion, 1 hemizygous DDX53 full gene deletion, and 1 homozygous, intragenic STK11 deletion. High-level mosaicism for X chromosome disomy (~ 10% 46,XY and ~ 90% 47,XXY) was also identified in 3 of 41 NOA patients who previously tested normal with conventional karyotyping. The remaining 24 CNVs detected were heterozygous, autosomal recessive carrier variants. Follow-up WES analysis confirmed 8 of 27 (30%) CNVs (X chromosome disomy excluded). WES analysis additionally identified 13 significant SNVs and/or indels in 9 patients (~ 9%) including X-linked AR, KAL1, and NR0B1 variants.

CONCLUSION

Using a combined genome-wide aCGH/WES approach, we identified pathogenic and likely pathogenic SNVs and CNVs in 15 patients (15%) with unexplained SPGF. This value equals the detection rate of conventional testing for aneuploidies and is considerably higher than the prevalence of Y chromosome microdeletions. Our results underscore the importance of comprehensive genomic analysis in emerging diagnostic testing of complex conditions like male infertility.

Abstract P4-09-06: Analyzing the changes in the HR+/HER2- metastatic breast cancer (mBC) landscape since the arrival of CDK4/6 inhibitors with machine learning and visual analytics

BACKGROUND: The real-world impact of CDK4/6 inhibitor use on HR+/HER2- mBC treatment sequencing, treatment response, and therapeutic utilization is limited. This study sought to describe treatment sequencing and response pre- and post-FDA approval of CDK4/6 inhibitors by conducting a traditional observational study approach and supplementing with a machine-learning methodology.

METHODS: Female patients ≥18yrs were identified in the MarketScan Commercial and Medicare Supplement databases with continuous enrollment for at least 12 months pre-index, ≥2 medical claims for a BC diagnosis and ≥2 medical claims for metastatic disease (earliest=index date), and who had no treatment at any time with HER2 targeted therapy. Patients were excluded if they had received CDK4/6 or everolimus treatment prior to index. Treatment was stratified by line of therapy pre- and post- first CDK4/6 approval (February 3, 2015). We identified treatment patterns with standard distributions and visual analytics. Response to therapy and utilization was analyzed with prediction models and IBM Watson® machine learning population comparison models.

RESULTS: A total of 19,558 patients were eligible for the study with a mean age at diagnosis of mBC of 62 (SD 13). Prior to first CDK4/6 inhibitor approval, anastrazole and letrozole monotherapies were most likely to be identified as both first and second line treatment. Following approval of the first CDK4/6 inhibitor in 2015, CDK4/6 inhibitors were observed as a first line treatment in 25% of patients, and as second line treatment in 24% of patients. Of patients diagnosed following the first CDK4/6 inhibitor approval, 44% of patients were exposed to endocrine therapy and 10% were exposed to chemotherapy in the pre-index period. Patients receiving CDK4/6 inhibitors in combination with endocrine therapy as first line treatment were observed to have a longer progression free survival time than patients receiving endocrine monotherapy. Visual analytics demonstrate a large variation in treatment sequencing, especially after first line therapy. Machine learning and prediction models identified a strong secular bias in the use of CDK4/6 and a signal for improved treatment response in patients with no exposure to endocrine therapies in the pre-index period.

CONCLUSIONS: The mBC treatment landscape has changed significantly with the introduction of CDK4/6 inhibitors, which may be expected to impact long-term outcomes. Visual analytics and machine learning approaches can improve clinical insight. These approaches can help with identifying patient and clinical characteristics that predict response and utilization as well as appropriate treatment selections across lines of therapy.

Citation Format: Meade D, Hensley Alford S, Mahatma S, Malangone-Monaco E, Boulanger L, Tkacz J, Turner SJ, Chen S, Manson S, Mejia S, Buleje I, Madan P, Kim G, Fowler R, Basar A. Analyzing the changes in the HR+/HER2- metastatic breast cancer (mBC) landscape since the arrival of CDK4/6 inhibitors with machine learning and visual analytics [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-09-06.

Effect of substituting soybean meal and canola cake with dried distillers grains with solubles at 2 dietary crude protein levels on feed intake, milk production, and milk quality in dairy cows

Dried distillers grain with solubles (DDGS) is an alternative source of feed protein for dairy cows. Previous studies found that DDGS, based on grains other than corn, can substitute for soybean meal and canola cake as a dietary protein source without reducing milk production or quality. As societal concerns exist, and in many areas strict regulation, regarding nitrogen excretion from dairy cows, the dairy industry has focused on reducing dietary protein level and nitrogen excretion. In the present study, we investigated the use of DDGS as a protein source, at a marginally low dietary crude protein (CP) levels, in a grass-clover and corn silage-based ration. The experiment involved 24 Holstein cows and 2 protein sources (DDGS or soybean-canola mixture) fed at 2 levels of CP (14 or 16%) in a 4 × 4 Latin square design. The aim of this study was to evaluate the effect of both protein source and protein level on feed intake, milk yield, and milk quality. The results indicated that feed intake, milk yield, and protein in milk increased when the protein level in the ration was 16% CP compared with 14%. We found no effect of substituting the soybean-canola mixture with DDGS. Moreover, no sensory problems were observed when comparing fresh milk with stored milk, and milk taste was unaffected by DDGS. Milk from cows fed DDGS had a slightly higher content of linoleic acid and conjugated linoleic acid (CLA 9-11), and lower content of C11 to C17 fatty acids than cows fed diets with the soybean-canola mixture. Cows fed the diets with 16% CP produced milk with higher oleic acids and lower palmitic acid content than cows fed 14% CP diets. To conclude, DDGS can substitute for a soybean-canola mixture without affecting feed intake, milk yield and quality, or sensory quality. Under the conditions of this experiment, feeding 16% CP compared with 14% CP in the ration can increase feed intake and milk production.

Effect of substituting soybean meal and canola cake with grain-based dried distillers grains with solubles as a protein source on feed intake, milk production, and milk quality in dairy cows

The growth of the bioethanol industry is leading to an increase in the production of coproducts such as dried distillers grains with solubles (DDGS). Both corn-based DDGS and grain-based DDGS (gDDGS; defined as originating from grain sources such as barley, wheat, triticale, or a mix, excluding corn) appear to be relevant sources of feed and protein for dairy cows. To date, most of the studies investigating DDGS have been performed with corn-based DDGS. The objectives of this study were to determine the effects of the proportion of gDDGS in the diet on feed intake, milk production, and milk quality. The present experiment involved 48 Holstein cows in a replicated 3 × 3 Latin square design with 3 grass-based dietary treatments consisting of 4, 13.5, and 23% gDDGS on a dry matter (DM) basis (L, M, and H, respectively) as a replacement for a concentrate mix. The concentrate mix consisted of soybean meal, canola cake, and beet pulp. Dry matter intake and energy-corrected milk yield were not affected by the proportion of gDDGS in the diet. Daily milk yield decreased with the H diet compared with the L and M diets. The percentage of fat in milk was higher when cows were fed the H diet compared with the L and M diets, whereas milk fat yield was not affected by dietary treatment. The M diet had a higher percentage of protein in milk compared with the L and H diets. Milk protein yield was similar for the L and M diets; however, it decreased for the H diet. Milk taste was not affected by the proportion of gDDGS in the diet or when milk was stored for 7 d. Linoleic acid and conjugated linoleic acid cis-9,trans-11 in milk increased with increasing proportion of gDDGS. To conclude, gDDGS can replace soybean meal and canola cake as a protein source in the diet of dairy cows. Up to 13.5% of the diet may consist of gDDGS without negatively affecting milk production, milk quality, or milk taste. When gDDGS represents 23% of dietary DM, milk production is reduced by 1.6 kg/d, whereas energy-corrected milk production is numerically reduced by 1 kg.

Relevance and complications of intravenous infusion at the emergency unit at Nice university hospital

OBJECTIVE

Insertion of peripheral venous catheters (PVCs) is current practice within the hospital environment and particularly in the emergency department (ED). This simple yet invasive technique may result in venous thrombosis, infection or mechanical complications. We conducted a prospective study at the Nice University Hospital ED in order to determine the frequency, relevance and complications of peripheral venous cannulation.

PATIENTS AND METHODS

Fourteen 24 h periods were surveyed over the months of May and June 2000, during which 2515 patients over 16 years of age attended the unit. Demographic and medical data were recorded for every patient who received a PVC. These patients were followed at 12 h intervals until the catheter was removed. Reasons for PVC, time left in place, and eventual complications were recorded. Justification for PVC was evaluated upon arrival at the ED, upon exiting the ED and in some cases within the hospital ward.

RESULTS

Six hundred and thirty of 2515 patients (25%) received a PVC (290 women (46%) and 340 men (54%); meanage 58 years). Indication for the PVC was considered unjustified in 24.8% of cases upon arrival at the ED, and 33.8% upon leaving the ED. Upon admission in a hospital ward after passing through the ED, out of 318 patients, the PVC was left in place for no reason in 63 (20%). Overall, 390 PVCs were followed until the time of their removal. Mean duration of IV infusion was 28 h. Among these 390 patients, 62 (15.9%) developed complications, of which 54 (13.6%) had thrombophlebitis and 9 (2.3%) developed local infection. Mean duration of PVC left in place for patients with complications was 50 h vs 25 h for patients with no complications (P<0.001).

CONCLUSION

Insertion of a PVC is common practice especially in EDs. The excessive use of this procedure leads to extra cost and iatrogenic complications. A renewed definition of its indication and raised awareness among hospital staff concerning the risks involved with this standard procedure should result in less use of PVC and fewer complications.