Abstract P4-05-16: Quality metric study of real-time targeted massive parallel sequencing (MPS) (ampliseq comprehensive cancer panel (CCP)) and bioinformatics in early breast cancer (EBC) using life technologies ion proton system

We undertook a prospective quality assurance and metric study in 26 women with early breast cancer (EBC) in order to identify issues that may interfere with real-time integration of massive parallel sequencing (MPS) with clinical and pathology parameters for clinical decision making.

Pre-operatively, patients underwent formal informed consent process with the aid of bespoke multimedia (iPad) technology to educate patients on a) the logistical aims of the trial b) somatic and hereditary genomics c) privacy and off target (non-cancer) issues.

On Day 1, seven patients (27%) underwent WLE & SNB, 17 (65%) WLE & AXLND, 2 (7%) Mastectomy & SNB.

Samples (tumour and normal) were collected fresh into Qiagen PaxGene Tissue Container preserving both morphology and biomolecules of the sample with lysis of tissues overnight.

Day 2&3; DNA extraction was performed using the Qiagen DSP kit over 1 hour.

DNA MPS CCP was performed on Life technologies Proton P1 chip using in-house modification of manufacturers protocol. The average time taken to run CCP includes 2 days library preparation; 4 hour sequencing run, 8 hours primary analysis for generating read alignments and sequencing files. The Ampliseq protocol required modifications with respect to template input amount and cycling parameters in order to increase the fidelity of library preparation. Limitations in sequencing depth and read qualities with the current technologies lend themselves to approximately 5-6 samples/sequencing run/day if 500x read depth per amplicon is desired.

Days 4-6 manually curated bioinformatics against publicly available mutation databases (e.g. COSMIC, ENSEMBL etc.)

Day 7 communication of results

Molecular Pathology results

The median age was 57, (32-84), 18 (72%) were postmenopausal. Histopathology invasive ductal 22 (84%), invasive lobular 2 (8%) metaplastic 2 (8%).

TNM Staging: T1b 5 (19%), T1c 9 (35%) T2 12 (46%); N0 23 (88%), N1mi 1 (4%), N1a 1 (4%), N2a 1 (4%).

Hormone receptors antibodies: ER (Roche SP1) Strong 20 (77%), Moderate 1 (4%), Weak 1 (4%), Negative 4 (15%); PR (Roche 1E2) Strong 11 (42%), Moderate 10 (38%), Weak 0 (0%), Negative 5 (19%); HER2 IHC (Ventana 4B5) Strong 1 (4%), Moderate 6 (23%), Weak 6 (23%), Negative 13 (50%); HER2 SISH (Ventana inform single probe); 1 SISH positive (mean copy number 29.6); 4 patients (15%) triple negative.

Molecular aberrations identified included oncogenes TP53 2 (8%), PIK3CA 12 (46%) HRAS 2 (8%), AKT1 1 (4%); tumour suppressor genes MLL3 2 (8%), MSH6 1 (4%), ARID1A 1 (4%), and in the germline in tumour suppressor genes EPHB6 1 (4%) and LTK 1 (4%).

Significant technical and bioinformatic challenges were encountered during the development of this metric study including Ampliseq protocol modification and parameter tuning for variant calling algorithm.

In summary, many challenges face the clinical laboratory developing high throughput MPS using desktop MPS. To date this is the first publication of the new Ion Proton P1 chips in development for real-time clinical decision making. Copy-number variation (CNV), RNA-Seq, Methyl-Seq data will be available for presentation at San Antonio.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-16.

Calcium supplementation prevents seasonal bone loss and changes in biochemical markers of bone turnover in elderly New England women: a randomized placebo-controlled trial

Elderly women are at increased risk for bone loss and fractures. In previous cross-sectional and longitudinal studies of women residing in northern latitudes, bone loss was most pronounced during winter months and in those consuming less than 1 g calcium per day. In this study we sought to test the hypothesis that calcium supplementation by either calcium carbonate or dietary means would prevent seasonal bone loss and preserve bone mass. Sixty older postmenopausal women without osteoporosis were randomized to one of three treatment arms: Dietary milk supplementation (D-4 glasses of milk/day), Calcium carbonate (CaCO3-1000 mg/day in two divided doses), or placebo (P). After 2 yr, placebo-treated women consumed a mean of 683 mg/day of calcium and lost 3.0% of their greater trochanteric (GT) bone mineral density (BMD) (P < 0.03 vs. baseline); Dietary supplemented women averaged a calcium intake of 1028 mg/day and sustained minimal loss from the GT (-1.5%; P = 0.30), whereas CaCO3-treated women (total Ca intake, 1633 mg/day) suffered no bone loss from the GT and showed a significant increase in spinal and femoral neck BMD (P < 0.05). Femoral bone loss occurred exclusively during the two winters of the study (i.e. total loss, -3.2%; P < 0.02 in placebo-treated women) with virtually no change in GT BMD during summer. Serum 25-OH vitamin D declined by more than 20% (P < 0.001) in all groups during the winter months but returned to baseline in summer; PTH levels rose approximately 20% (P < 0.001) during winter but did not return to baseline during the summers. Urine N-telopeptide and osteocalcin levels increased significantly but only in the P-treated women and only during winter. Serum insulin growth factor binding protein 4, an inhibitory insulin growth factor binding protein, rose 15% (P < 0.03) from summer to winter, but this increase was significant only in those women consuming <1000 mg/day of calcium. By multivariate analysis, total calcium intake was the strongest predictor of bone loss from the hip. Urinary N-telopeptide also closely correlated with GT BMD but only during winter (P = 0.003). We conclude that calcium supplementation prevents bone loss in elderly women by suppressing bone turnover during the winter when serum 25-OH vitamin D declines and serum PTH increases. The precise amount of calcium necessary to preserve BMD in elderly women requires further studies, although in this study, at least 1000 mg/day of supplemental calcium was adequate prophylaxis against femoral bone loss.

Elderly women in northern New England exhibit seasonal changes in bone mineral density and calciotropic hormones

A seasonal component to bone loss has been reported in some postmenopausal women. We hypothesized that elderly women in northern New England would be at high risk for bone loss during winter because of their age, diet and lack of sunlight. Eighteen elderly but healthy women (mean age 77 years) started a 2-year observational study in a remote area of northwestern Maine (Greenville: 45.5 degrees N latitude). Fifteen women completed the study. Bone mineral density of the spine (L-BMD) and hip (F-BMD) and biochemical markers of bone turnover were measured biannually. In vitro photo-conversion of provitamin D3 to previtamin D3 was determined in the winter and spring. Initial calcium and vitamin D intake averaged 700 +/- 72 mg/day and 6.2 +/- 1.2 micrograms/day, respectively. During the first year L-BMD dropped 4.2% (P = 0.002) while F-BMD dropped 2.4% (P = 0.09), primarily because of steep declines during the fall and winter (August to February: L-BMD: 3.6%, P = 0.001; F-BMD: 3.0%, P = 0.04). In that 6-month period, serum 25 hydroxyvitamin D (25(OH)D) fell 13 +/- 6% (P = 0.06) and PTH rose 27 +/- 11% (P = 0.01). Additionally, there was no detectable in vitro conversion of provitamin D to previtamin D over 8 h of one sunny winter day. In the summer, PTH and 25(OH)D reverted to basal levels and significant in vitro photoconversion of provitamin D to previtamin D was detected. In the 2nd year of the study, vitamin D consumption increased (+2.0 +/- 1.2 micrograms/day, P = 0.03 vs. baseline), L-BMD increased slightly (+1.8%, P = 0.05) and F-BMD did not change (+0.5%, P = NS). Again, changes in BMD and vitamin D were seasonal: L-BMD and F-BMD were constant during fall and winter but both sites showed increases during summer (L-BMD: +1.7%, P = 0.04, F-BMD: +1.6%, P = 0.25). In the second winter, serum 25(OH)D fell nearly 20% and PTH rose 17%. Increased dietary consumption of vitamin D was positively correlated with changes in F-BMD at 18 months (r = 0.61, P = 0.02) and resulted in slightly greater serum 25(OH)D concentrations during the second winter than the first. The difference in serum 25(OH)D between the first and second winter was the strongest predictor of lumbar bone accretion during the second year of the study (r = 0.59, P = 0.04). In this 24-month observational study, significant seasonal changes in BMD, 25(OH)D and PTH were reported.(ABSTRACT TRUNCATED AT 250 WORDS)

Outbreak of hypersensitivity pneumonitis among mushroom farm workers

Between April 1982 and August 1985, seven cases of mushroom worker's lung (MWL), a form of hypersensitivity pneumonitis, were diagnosed among workers at one mushroom farm in Florida. The cases suffered from episodic shortness of breath, cough, fever and chills, myalgia, malaise, and difficulty breathing. Pulmonary function testing revealed restrictive ventilatory impairment and reduced diffusing capacity; chest radiographs exhibited diffuse interstitial pulmonary infiltrates. The seven cases occurred among workers from different farm operations, suggesting that workers throughout the farm were exposed to the disease causing agent(s). Six of the affected workers left employment at the farm in order to remain free of symptoms. The other affected worker was able to continue working at the farm, but only by remaining in a maintenance shop which was physically separated from the rest of the farm facilities. An industrial hygiene survey demonstrated that farm workers from every work area were exposed to organic dust constituents suspected of causing MWL, but no specific antigens were identified as the cause of the cases. Of the remaining workers who participated in a cross-sectional respiratory morbidity survey at the farm, approximately 20% of the more heavily exposed workers reported occasionally experiencing symptoms consistent with MWL. Approximately 10% of the workers had below normal spirometry test results, but interpretation was hampered by the diverse racial makeup of the population and lack of an adequate comparison group. No abnormalities consistent with either acute or chronic MWL were seen on the chest radiographs. Serologic tests demonstrated that almost all workers had been exposed to antigens capable of causing MWL, but the results were not associated with health status. At the time of the cross-sectional survey, no workers were found to be suffering acute respiratory problems consistent with MWL.

Hosts on which nymphal Ixodes ricinus most abundantly feed

To identify hosts that may serve as European reservoirs for the agent of Lyme disease, Borrelia burgdorferi, we determined whether nymphal Ixodes ricinus feed mainly on particular mice (Apodemus flavicollis or A. agrarius), voles (Clethrionomys glareolus) or on sand lizards (Lacerta agilis) and whether the abundance of these hosts corresponds to the seasonal activity of the subadult stages of the vector tick. In all sites, the mice appeared most heavily infested by larvae; at least seven parasitized each mouse, about three per vole and four per lizard. Many fewer nymphal I. ricinus parasitized A. flavicollis and C. glareolus than did larvae. Although more than 30 times as many larval than nymphal ticks parasitized the two most abundant hosts (C. glareolus and A. flavicollis), about 15 times as many fed on A. agrarius and twice as many on lizards. Nymphal and larval ticks fed on rodents at about the same time. Lizards were most abundantly parasitized by nymphs somewhat earlier than by larvae. Early in the season of transmission of Lyme disease, virtually all A. agrarius as well as lizards were potentially exposed to spirochetes borne by nymphal I. ricinus. We concluded that larval and nymphal I. ricinus differentially parasitize different hosts. Because so many of these nymphs feed on them, A. agrarius may more effectively serve as reservoirs for the agent of Lyme disease than do other putative reservoir hosts. The presence of lizards may inhibit transmission.

Evaluation of lupus anticoagulants: antiphospholipid antibodies, endothelium associated immunoglobulin, endothelial prostacyclin secretion, and antigenic protein S levels

Plasma samples from nineteen patients with well characterized lupus anticoagulants (LA) were evaluated using a series of test systems. An ELISA was used to determine if the plasmas contained antiphospholipid antibodies (APA); fifteen of nineteen LA plasmas contained APA, with five exhibiting IgG only, two exhibiting IgM, and eight plasmas containing both IgG and IgM. Anti-phosphatidyl serine (PS) was the predominant IgG specificity and all IgM APA-containing plasmas reacted with phosphatidyl inositol (PI). An ELISA was developed to determine if LA plasmas contained immunoglobulin which would associate with cultured human umbilical cord vein-derived endothelial cells (HUV); ten of nineteen plasmas contained endothelium associated immunoglobulin (EAI). There was significant concordance between the occurrence of EAI and IgM anti-PI. The occurrence of EAI or APA, either singly or in combination, did not correlate with a past history of thrombosis. Patient plasmas were incubated with HUV and examined for effects on HUV prostacyclin (PGI2) secretion; six plasmas significantly stimulated PGI2 secretion and one plasma was inhibitory. Finally, plasma levels of free and total antigenic protein S were determined by EID. Five plasmas contained significantly reduced levels of free antigenic protein S, and total antigenic protein S was reduced in ten plasmas. Patient histories were examined for evidence of thrombotic episodes; six patients had a history of either arterial or venous thrombosis, with five of these six patients having drug-induced LA. Thus, unlike previous studies, drug-induced LA were associated with thrombosis.

Factor VIII assays. Assessment of variables

Factor VIII assays are the most common specific coagulation factor assay performed in the United States. Interlaboratory proficiency studies have documented persistent problems with variation in results between laboratories. The Coagulation Resource Committee of the College of American Pathologists conducted a workshop to analyze variables that may affect performance of the one-stage factor assay. The results indicate that accuracy of the assay can be improved by uniform standardization of reference plasma samples and that reproducibility can be enhanced through appropriate choice of reagents and instruments. Optimizing performance of this assay should lead to more reproducible interlaboratory results.

The sensitivity of different coagulation reagents to the presence of lupus anticoagulants

The sensitivity and responsiveness of seven activated partial thromboplastin time reagents to the presence of lupus anticoagulants (LAs) was evaluated with a panel of 50 well-characterized LA plasmas. The results document that some reagents are clearly less responsive and sensitive to LAs; however, there is considerable variability between individual LA samples in these features. In addition, with 16% of these samples, immediate mixing studies showed correction of the activated partial thromboplastin time to the normal range with a 1:1 mixture of normal and LA plasma and 8% to 10% showed either a normal platelet neutralization procedure or a normal tissue thromboplastin inhibition procedure. Together, these findings provide further evidence of the laboratory heterogeneity of these inhibitors. The effect of this variability on the diagnosis of these inhibitors is discussed.