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Supplementary Tables 1-3. Supplementary Table 1. Use of cobas-like partial HPV typing in triage of ASC-US. Supplementary Table 2. Use of cobas-like partial HPV typing in co-testing. Supplementary Table 3. Use of cobas-like partial HPV typing in primary HPV testing

Background: The cobas HPV Test (“cobas”; Roche Molecular Systems) detects HPV16 and HPV18 individually, and a pool of 12 other high-risk (HR) HPV types. The test is approved for (i) atypical squamous cells of undetermined significance (ASC-US) triage to determine need for colposcopy, (ii) combined screening with cytology (“cotesting”), and (iii) primary HPV screening.Methods: To assess the possible value of HPV16/18 typing, >17,000 specimens from a longitudinal cohort study of initially HPV-positive women (HC2, Qiagen) were retested with cobas. To study accuracy, cobas genotyping results were compared with those of an established method, the Linear Array HPV Genotyping Test (LA, Roche Molecular Systems). Clinical value of the typing strategy was evaluated by linking the cobas results (supplemented by other available typing results) to 3-year cumulative risks of CIN3+.Results: Grouped hierarchically (HPV16, else HPV18, else other HR types, else negative), the κ statistic for agreement between cobas and LA was 0.86 [95% confidence interval (CI), 0.86–0.87]. In all three scenarios, HPV16-positive women were at much higher 3-year risk of CIN3+ than HPV16-negative women: women ages 21 and older with ASC-US (14.5%; 95% CI, 13.5%–15.5% vs. 3.5%; 95% CI, 3.3–3.6); women ages 30 years and older that were HPV-positive cytology-negative (10.3%; 95% CI, 9.6–11.1 vs. 2.3%; 95% CI, 2.2–2.4); and all women 25 years and older that were HPV-positive (18.5%; 95% CI, 17.8–19.2 vs. 4.3%; 95% CI, 4.2–4.4).Conclusion: The cobas and LA results show excellent agreement. The data support HPV16 typing.Impact: HPV16 typing is useful in the management of HPV-positive/cytology-negative women in cotesting, of all HPV-positive women in primary HPV testing, and perhaps in the management of HPV-positive women with ASC-US. Cancer Epidemiol Biomarkers Prev; 24(9); 1304–10. ©2015 AACR.See related commentary by Del Mistro, p. 1302

This qualitative case study tells the story of Jack's turn to multimodal tools in second grade. Jack's mom, who is also the researcher, analyzes his paper/pencil and digital book reports during second grade to show how whole language practices, driven by his interests, opened possibilities that his teacher and mom never imagined he would be capable of in second grade. Not only did he enjoy digital writing more than traditional paper/pencil writing, but he also demonstrated greater sentence fluency, stronger analysis, and connected more meaningfully with his readers. Additionally, the digital mode opened up a dialog between student and teacher that facilitated a healthier writing process. This analysis has the potential to help teachers and parents imagine broader possibilities for using digital tools to facilitate healthy literacy practices at home and at school.

Academic literacy and student diversity: The case for inclusive practice Ursula Wingate (2015) ISBN-13: 978-1783093472. Pp. 208. Genre-based automated writing evaluation for L2 research writing: From design to evaluation and enhancement Elena Cotos (2014) ISBN-13: 978-1137333360. Pp. 302.

Background: The cobas HPV Test (“cobas”; Roche Molecular Systems) detects HPV16 and HPV18 individually, and a pool of 12 other high-risk (HR) HPV types. The test is approved for (i) atypical squamous cells of undetermined significance (ASC-US) triage to determine need for colposcopy, (ii) combined screening with cytology (“cotesting”), and (iii) primary HPV screening. Methods: To assess the possible value of HPV16/18 typing, >17,000 specimens from a longitudinal cohort study of initially HPV-positive women (HC2, Qiagen) were retested with cobas. To study accuracy, cobas genotyping results were compared with those of an established method, the Linear Array HPV Genotyping Test (LA, Roche Molecular Systems). Clinical value of the typing strategy was evaluated by linking the cobas results (supplemented by other available typing results) to 3-year cumulative risks of CIN3+. Results: Grouped hierarchically (HPV16, else HPV18, else other HR types, else negative), the κ statistic for agreement between cobas and LA was 0.86 [95% confidence interval (CI), 0.86–0.87]. In all three scenarios, HPV16-positive women were at much higher 3-year risk of CIN3+ than HPV16-negative women: women ages 21 and older with ASC-US (14.5%; 95% CI, 13.5%–15.5% vs. 3.5%; 95% CI, 3.3–3.6); women ages 30 years and older that were HPV-positive cytology-negative (10.3%; 95% CI, 9.6–11.1 vs. 2.3%; 95% CI, 2.2–2.4); and all women 25 years and older that were HPV-positive (18.5%; 95% CI, 17.8–19.2 vs. 4.3%; 95% CI, 4.2–4.4). Conclusion: The cobas and LA results show excellent agreement. The data support HPV16 typing. Impact: HPV16 typing is useful in the management of HPV-positive/cytology-negative women in cotesting, of all HPV-positive women in primary HPV testing, and perhaps in the management of HPV-positive women with ASC-US. Cancer Epidemiol Biomarkers Prev; 24(9); 1304–10. ©2015 AACR. See related commentary by Del Mistro, p. 1302

The effective management of women with human papillomavirus (HPV)-positive, cytology-negative results is critical to the introduction of HPV testing into cervical screening. HPV typing has been recommended for colposcopy triage, but it is not clear which combinations of high-risk HPV types provide clinically useful information. This study included 18,810 women with Hybrid Capture 2 (HC2)-positive, cytology-negative results and who were age ≥30 years from Kaiser Permanente Northern California. The median follow-up was 475 days (interquartile range [IQR], 0 to 1,077 days; maximum, 2,217 days). The baseline specimens from 482 cases of cervical intraepithelial neoplasia grade 3 or cancer (CIN3+) and 3,517 random HC2-positive noncases were genotyped using 2 PCR-based methods. Using the case-control sampling fractions, the 3-year cumulative risks of CIN3+ were calculated for each individual high-risk HPV type. The 3-year cumulative risk of CIN3+ among all women with HC2-positive, cytology-negative results was 4.6%. HPV16 status conferred the greatest type-specific risk stratification; women with HC2-positive/HPV16-positive results had a 10.6% risk of CIN3+, while women with HC-2 positive/HPV16-negative results had a much lower risk of 2.4%. The next most informative HPV types and their risks in HPV-positive women were HPV33 (5.9%) and HPV18 (5.9%). With regard to the etiologic fraction, 20 of 71 cases of cervical adenocarcinoma in situ (AIS) and adenocarcinoma in the cohort were positive for HPV18. HPV16 genotyping provides risk stratification useful for guiding clinical management; the risk among HPV16-positive women clearly exceeds the U.S. consensus risk threshold for immediate colposcopy referral. HPV18 is of particular interest because of its association with difficult-to-detect glandular lesions. There is a less clear clinical value of distinguishing the other high-risk HPV types.

Purpose Metastatic pancreatic ductal adenocarcinoma is characterized by excessive hyaluronan (HA) accumulation in the tumor microenvironment, elevating interstitial pressure and impairing perfusion. Preclinical studies demonstrated pegvorhyaluronidase alfa (PEGPH20) degrades HA, thereby increasing drug delivery. Patients and Methods Patients with previously untreated metastatic pancreatic ductal adenocarcinoma were randomly assigned to treatment with PEGPH20 plus nab-paclitaxel/gemcitabine (PAG) or nab-paclitaxel/gemcitabine (AG). Tumor HA levels were measured retrospectively using a novel affinity histochemistry assay. Primary end points were progression-free survival (PFS; overall) and thromboembolic (TE) event rate. Secondary end points included overall survival, PFS by HA level, and objective response rate. An early imbalance in TE events in the PAG arm led to a clinical hold; thereafter, patients with TE events were excluded and enoxaparin prophylaxis was initiated. Results A total of 279 patients were randomly assigned; 246 had HA data; 231 were evaluable for efficacy; 84 (34%) had HA-high tumors (ie, extracellular matrix HA staining ≥ 50% of tumor surface at any intensity). PFS was significantly improved with PAG treatment overall (hazard ratio [HR], 0.73; 95% CI, 0.53 to 1.00; P = .049) and for patients with HA-high tumors (HR, 0.51; 95% CI, 0.26 to 1.00; P = .048). In patients with HA-high tumors (PAG v AG), the objective response rate was 45% versus 31%, and median overall survival was 11.5 versus 8.5 months (HR, 0.96; 95% CI, 0.57 to 1.61). The most common treatment-related grade 3/4 adverse events with significant differences between arms (PAG v AG) included muscle spasms (13% v 1%), neutropenia (29% v 18%), and myalgia (5% v 0%). TE events were comparable after enoxaparin initiation (14% PAG v 10% AG). Conclusion This study met its primary end points of PFS and TE event rate. The largest improvement in PFS was observed in patients with HA-high tumors who received PAG. A similar TE event rate was observed between the treatment groups in stage 2 of the trial.

The cobas human papillomavirus (HPV) test (cobas) was recently approved by the U.S. Food and Drug Administration (FDA) and identifies HPV16 and HPV18 separately as well as detecting a pool of 11 HR-HPV genotypes (HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -68) and also HPV66. We compared cobas, Linear Array (LA), and Hybrid Capture 2 (HC2) assays for detection of carcinogenic HPV DNA, and cobas and LA for detection of HPV16 and HPV18 DNA, among the first 1,852 women enrolled in the HPV Persistence and Progression Cohort (PaP Cohort) study. Specimens were tested by all 3 assays 1 year after an HC2-positive result. In 1,824 specimens with cobas results, cobas had an 85.9% agreement with HC2 and 91.0% agreement with LA for carcinogenic HPV detection. When results between cobas and HC2 disagreed, cobas tended to call more women HPV positive ( P < 0.01). Categorizing cobas and LA results hierarchically according to cancer risk (HPV16, HPV18, other carcinogenic HPV genotypes, or carcinogen negative), there was a 90% agreement for all categories of HPV ( n = 1,824). We found good agreement between the two U.S. FDA-approved HPV tests, with discrepancies between the two assays due to specific characteristics of the individual assays. Additional studies are needed to compare HC2 and cobas for detecting and predicting CIN3 to understand the clinical implications of the discrepant test results between the two tests.

Results from a prototype real-time PCR assay that separately detected human papillomavirus genotype 16 (HPV16), HPV18, and 12 other carcinogenic HPV genotypes in aggregate (cobas 4800 HPV test) and results from a PCR assay that detects 37 HPV genotypes individually (Linear Array) were compared using a convenience sample of cervical specimens ( n = 531). The percentage of total agreement between the two assays was 94.7% (95% confidence interval, 92.5 to 96.5%). The Linear Array test was more likely than cobas 4800 HPV test to test positive for the 12 other carcinogenic HPV genotypes among women without evidence of cervical disease ( P = 0.004).

The HLA-G gene is primarily expressed in placental cells that invade the maternal decidua during pregnancy. This gene encodes multiple isoforms that fulfill a variety of functions at the maternal-fetal interface throughout gestation. Recently, a null allele for the most abundant HLA-G isoform was associated with recurrent miscarriage in two independent studies, suggesting that reduced levels of the HLA-G1 protein may compromise successful pregnancy. We initiated the present study to determine whether other polymorphisms that could affect expression levels of HLA-G were associated with fetal loss in women participating in a 15-year prospective study of pregnancy outcome. We genotyped these subjects for 18 single-nucleotide polymorphisms in the 1,300 bp upstream of exon 1, 13 of which were identified as part of this study, as well as for an insertion/deletion (in/del) polymorphism in the 3′ untranslated region. The 18 SNPs defined eight unique haplotypes. One polymorphism, −725C/G, was associated with fetal loss, with an increased risk for miscarriage in couples in which both partners carried the −725G allele, compared with couples not carrying this allele (odds ratio 2.76, 95% confidence interval 1.08–7.09; P=.035). Further, the G at nucleotide −725 creates a CpG dinucleotide, and we demonstrate that this CpG site is methylated on −725G alleles. Overall, this study identified extraordinary levels of variation in the 5′-upstream regulatory region of HLA-G and provides evidence for an association between a promoter-region SNP and fetal loss rates, further attesting to the novel features and critical role of this gene in pregnancy.

e23196 Background: Enzymatic degradation of hyaluronan (HA) by PEGylated recombinant human hyaluronidase PH20 (PEGPH20) induces a remodeling of the tumor microenvironment that impacts tumor behavior and response to therapy. Ventana Medical Systems, Inc., (VMSI) and Halozyme Therapeutics co-developed the VENTANA HA RxDx Assay and a scoring method to evaluate HA in solid tumors to potentially predict which patients might better respond to the addition of PEGPH20 to cancer treatments. Methods: Using Halozyme’s novel recombinant HA binding probe altered to include a rabbit Fc region, VMSI developed a highly specific and sensitive affinity histochemistry assay that binds to HA in tissues. Histological features and staining patterns of 106 samples from Halozyme’s 109-202 Phase 2 study of PEGPH20 combined with nab-paclitaxel plus gemcitabine (AG) vs. AG alone in patients with previously untreated stage IV pancreatic ductal adenocarcinoma (PDA) with clinical outcome data were analyzed to develop a scoring method evaluating HA accumulation. Results: A novel scoring algorithm focused solely on the extracellular matrix (ECM) was developed. An ECM HA staining ≥ 50% of the entire tumor surface at any intensity defines an HA-High PDA. We recommend that a 0.05 cm x 0.2 cm uninterrupted fragment of tumor cells and associated stroma obtained using needle gauges of 16 to 20 G as the minimally required amount of tissue to assess HA in PDA. Based on verification studies performed by VMSI, including an inter-reader precision study with a 94% agreement rate, VMSI scoring method proved to be trainable, reproducible, and transferable to pathologists, supporting an IDE approval for selecting patients in the Phase 3 HALO 109-301 study. Conclusions: Performance of the VENTANA HA RxDx Assay, a robust affinity histochemical assay, has been successfully verified in PDA. Two Halozyme clinical studies in PDA (Phase 2 HALO 109-202 Stage 2 & ongoing Phase 3 HALO 109-301) are expected to validate the VMSI HA scoring method in selecting patients who might better respond to the addition of PEGPH20 to cancer treatments. Current Phase 1/2 studies are exploring the utility of the VENTANA HA RxDx Assay and the pantumor potential of PEGPH20.

4008 Background: Hyaluronan (HA) accumulation in the tumor microenvironment produces elevated tumor pressure, vascular compression, and reduced drug delivery. PEGPH20 degrades HA, increasing the access and therapeutic index of anticancer agents. Methods: In Stage 1 of this phase II study, pts with untreated mPDA were randomized 1:1 to PAG (P; 3 µg/kg IV 2x/wk x 3 wks in C1, then 1x/wk x 3 wks in C2+, plus AG) vs AG every 28 days. An imbalance in thromboembolic (TE) events in the PAG arm led to a clinical hold (~40% of pts discontinued PEGPH20), exclusion of pts at high risk for TE events and enoxaparin prophylaxis in both study arms. In Stage 2, randomization was 2:1 to PAG vs AG. Tumor HA was tested using a novel assay (VENTANA HA RxDx). Primary endpoints were PFS (evaluable pts) and TE event rate (Stage 2). Secondary endpoints were PFS by HA level and ORR. Results: 279 pts were randomized; 231 are evaluable for efficacy. Of 246 pts with HA data, 84 (34%) were HA-High. As of December 16, 2016, the primary PFS endpoint was statistically significant for PAG vs AG (HR 0.73, 95% CI 0.53-1.00; p = 0.048) (Table). PFS in HA-High pts was also statistically significant in the PAG vs AG arm (HR 0.51; 95% CI 0.26-1.00; p = 0.048). ORR in HA-High pts was 46% (PAG) vs 34% (AG). Overall survival in HA-High pts (exploratory) was 11.5 months (mo) (PAG) and 8.5 mo (AG) (HR 0.96, 95% CI 0.57-1.61). TE events were similar (PAG 14% vs AG 10%) following enoxaparin initiation. All grade treatment-related AE included peripheral edema (PAG 63% vs AG 26%), muscle spasms (56% vs 3%), neutropenia (34% vs 19%), and myalgia (26% vs 7%). Conclusions: Randomized Phase II study met both primary endpoints (PFS and TE event rate), with the largest improvement in the secondary endpoint of PFS in HA-High pts. These data support HA as a potential predictive biomarker for patient selection of PEGPH20, currently investigated in the ongoing global Phase III HALO 301 study with PFS and OS as co-primary endpoints. Clinical trial information: NCT01839487. [Table: see text]

Modulation of the expression of genes of the major histocompatibility complex (MHC) in tissues at the maternal-fetal interface almost certainly plays a role in successful development of the semi-allogeneic fetus. While expression of the classical class I genes (HLA-A, B, C) is low to non-existent at this site, the non-classical molecule, HLA-G, is expressed uniquely in fetal cells at the maternal-fetal interface. The recent demonstration that homozygotes for a deletion mutation in exon 3 (1597DeltaC) of HLA-G do not express the full-length HLA-G1 isoforms indicates a potential reduction in expression of this isoform in heterozygotes. If the full-length isoform of HLA-G (i.e. HLA-G1) contributes to proper invasion of maternal spiral arteries by extravillous cytotrophoblast, then 1597DeltaC heterozygotes could be at increased risk for disorders of trophoblast invasion. Two populations, infants with intrauterine growth retardation (IUGR) and infants of preeclamptic (PE) mothers, were genotyped for the 1597DeltaC polymorphism. The frequency of 1597DeltaC in these samples was not significantly different from healthy controls, suggesting that heterozygotes for this deletion mutation are not at significantly increased risk for PE or IUGR (P = 0.727 and 0.803, respectively).

HLA-G is a non-classical class Ib gene with many unusual features. Because of its unique expression pattern, which is primarily limited to fetal cells at the maternal fetal interface, this gene has gained the attention of many investigators. In this paper we review some of the novel features of HLA-G, with particular reference to polymorphic variants in the gene, and discuss the implications of these features for the potential function and evolutionary history of HLA-G.

e15749Background: Ventana Medical Systems, Inc. is developing in collaboration with Halozyme Therapeutics an affinity histochemical companion diagnostic to aid in selecting patients with pancreatic...

4104Background: Poor outcome in pancreatic ductal adenocarcinoma (PDA) is associated partly with stromal hyaluronan (HA) accumulation, which compromises chemotherapy perfusion. PEGPH20 (PEGylated r...

Human papillomavirus (HPV) is a causal agent of cervical cancer, and persistent HPV16 or HPV18 infection carries a particularly high risk. The cobas HPV Test (cobas) provides individual HPV16/HPV18 genotyping with a simultaneous result for 12 other high-risk HPV (hrHPV) genotypes. Its analytical performance for hrHPV genotype detection was retrospectively evaluated against the digene Hybrid Capture 2 HPV DNA test (HC2), in three European centers, in 1360 cervical samples. Both HPV tests performed similarly, with no significant difference in the number of positive and negative samples identified by each test and good agreement between the tests was observed. Discordant samples were analyzed with the Linear Array HPV genotyping test. More low-risk HPV (lrHPV) genotypes were detected in HC2-positive/cobas-negative samples compared with HC2-negative/cobas-positive samples. Conversely, more hrHPV genotypes were detected in HC2-negative/cobas-positive samples compared with HC2-positive/cobas-negative samples. Eight HC2-negative/cobas-positive samples were positive for HPV16 compared with five HC2-positive/cobas-negative samples; HPV18 was detected in one HC2-negative/cobas-positive sample and one HC2-positive/cobas-negative sample. The cobas HPV Test demonstrates comparable analytical performance to the HC2 test, but with a lower rate of cross-reactivity with lrHPV genotypes, and has the advantage of simultaneously providing HPV16/HPV18 identification.

HLA-G is a non-classical human leukocyte antigen expressed primarily in fetal tissues at the maternal-fetal interface. This expression pattern is unique among HLA genes and suggests that HLA-G may be involved in interactions that are critical in establishing and/or maintaining pregnancy. To evaluate the role of polymorphisms at this locus in maternal-fetal interactions, 113 couples with unexplained recurrent miscarriage were genotyped for seven polymorphisms that define 12 HLA-G alleles. Logistic regression analysis was used to assess whether HLA-G genotypes were associated with an increased risk for a subsequent miscarriage. The presence of an HLA-G*0104 or HLA-G*0105N allele in either partner was significantly associated with an increased risk for miscarriage, after adjustment for maternal age, number of previous miscarriages, history of a previous liveborn, and treatment with paternal mononuclear cells. The *0104 and *0105N alleles are defined by polymorphisms in the alpha-2 domain and encode protein variants that are present only in the full-length HLA-G1 protein. The significant genotype-specific risk in this population suggests that allelic variation in the alpha-2 domain of the HLA-G1 isoforms contributes to recurrent miscarriage.

HLA-G is a nonclassical, class I HLA gene that is primarily expressed by fetal cells at the maternal-fetal interface and is thought to play a key role in the induction of tolerance in pregnancy. This paper reports the identification of a single base pair deletion at position 1597 (1597de1C) in exon 3 (encoding the α2-domain) of HLA-G on 20 of 272 (7.4 per cent) African American chromosomes, three of 102 (2.9 per cent) Hispanic chromosomes, and none of 134 Caucasian chromosomes. This relatively common frameshift mutation results in amino acid substitutions in all of the residues in the second half of exon 3 including the conserved cysteine at codon 164. An adult individual was identified who was homozygous for this ‘null’ allele, and a first trimester placenta that was homozygous for 1597de1C had no detectable HLA-G1 protein. These data indicate that expression of HLA-G1 protein is not essential for fetal survival.