Making decisions in missing person identification cases with low statistical power

The present work proposes a general strategy for dealing with missing person identification cases through DNA-database search. Our main example is the identification of abducted children in the last civic-dictatorship of Argentina, known as the "Missing Grandchildren of Argentina". Particularly we focus on those pedigrees where few, or only distant relatives of the missing person are available, resulting in low statistical power. For such complex cases we provide a statistical method for selecting a likelihood ratio (LR) threshold for each pedigree based on error rates. Furthermore, we provide an open-source user friendly software for computing LR thresholds and error rates. The strategy described in the paper could be applied to other large-scale cases of DNA-based identification hampered by low statistical power.

Does prolonged labor affect the birth experience and subsequent wish for cesarean section among first-time mothers? A quantitative and qualitative analysis of a survey from Norway

Background

Prolonged labor might contribute to a negative birth experience and influence first-time mothers’ attitudes towards future pregnancies. Previous studies have not adjusted for possible confounding factors, such as operative delivery, induction and postpartum hemorrhage. We aimed to determine the impact of prolonged labor on birth experience and a wish for cesarean section in subsequent pregnancies.

Methods

A survey including the validated “Childbirth Experience Questionnaire”. First-time mothers giving birth between 2012 and 2014 at a Norwegian university hospital participated. Data from deliveries were collected. Regression analysis and thematic content analysis were performed.

Results

459 (71%) women responded. Women with labor duration > 12 h had significantly lower scores on two out of four sub-items of the questionnaire: own capacity (p = 0.040) and perceived safety (p = 0.023).

Other factors contributing to a negative experience were:

Cesarean section vs vaginal birth: own capacity (p = 0.001) and perceived safety (p = 0.007). Operative vaginal vs spontaneous birth: own capacity (p = 0.001), perceived safety (p < 0.001) and participation (p = 0.047).

Induced vs spontaneous start: own capacity (p = 0.039) and participation (p = 0.050). Postpartum hemorrhage ≥500 ml vs < 500 ml: perceived safety (p = 0.002) and participation (p = 0.031).

In the unadjusted analysis, prolonged labor more than doubled the risk (odds ratio (OR) 2.66, 95%CI 1.42–4.99) of a subsequent wish for cesarean delivery. However, when adjustments were made for mode of delivery and induction, emergency cesarean section (OR 8.86,95%CI 3.85–20.41) and operative vaginal delivery (OR 3.05, 95%CI 1.46–6.38) remained the only factors significantly increasing the probability of wanting a cesarean section in subsequent pregnancies.

The written comments on prolonged labor (n = 46) indicated four main themes:

Difficulties gaining access to the labor ward.

Being left alone during the unexpectedly long, painful early stage of labor.

Stressful operative deliveries and worse pain than imagined.

Lack of support and too little or contradictory information from the staff.

Conclusions

Women with prolonged labors are at risk of a negative birth experience. Prolonged labor per se did not predict a wish for a cesarean section in a subsequent pregnancy. However, women with long labors more often experience operative delivery, which is a risk factor of a later wish for a cesarean section.

Pairwise relatedness testing in the context of inbreeding: expectation and variance of the likelihood ratio

In this paper we investigate various effects of inbreeding on the likelihood ratio (LR) in forensic kinship testing. The basic setup of such testing involves formulating two competing hypotheses, in the form of pedigrees, describing the relationship between the individuals. The likelihood of each hypothesis is computed given the available genetic data, and a conclusion is reached if the ratio of these exceeds some pre-determined threshold. An important aspect of this approach is that the hypotheses are usually not exhaustive: The true relationship may differ from both of the stated pedigrees. It is well known that this may introduce bias in the test results. Previous work has established formulas for the expected value and variance of the LR, given the two competing hypotheses and the true relationship. However, the proposed method only handles cases without inbreeding. In this paper we extend these results to all possible pairwise relationships. The key ingredient is formulating the hypotheses in terms of Jacquard coefficients instead of the more restricted Cotterman coefficients. While the latter describe the relatedness between outbred individuals, the more general Jacquard coefficients allow any level of inbreeding. Our approach also enables scrutiny of another frequently overlooked source of LR bias, namely background inbreeding. This ubiquitous phenomenon is usually ignored in forensic kinship computations, due to lack of adequate methods and software. By leveraging recent work on pedigrees with inbred founders, we show how background inbreeding can be modeled as a continuous variable, providing easy-to-interpret results in specific cases. For example, we show that if true siblings are subjected to a test for parent-offspring, moderate levels of background inbreeding are expected to inflate the LR by more than 50%.

The CD34+ Cell Dose Matters in Hematopoietic Stem Cell Transplantation with Peripheral Blood Stem Cells from Sibling Donors

The effect of CD34⁺ cell dose in allogeneic hematopoietic stem cell transplantation (HSCT) on overall survival (OS) and incidence of acute and chronic graft-versus-host disease (GvHD) has not been established and few studies have been performed. Our single center analysis included 189 patients with hematological malignancies who received peripheral blood stem cell (PBSC) grafts from sibling donors. Myeloablative conditioning was used in 88 cases and 101 received reduced intensity conditioning. The median CD34⁺ cell dose was 5.6 × 10⁶/kg (0.6–17.0). In the multivariate analysis, a CD34 cell dose of 6–7 × 10⁶/kg was associated with better OS and lower transplant-related mortality (TRM), while a dose of <5 × 10⁶/kg led to increased relapse and reduced chronic GVHD (cGVHD). A high CD34 cell-dose (>6.5 × 10⁶/kg) correlated with less acute GVHD (aGVHD) II–IV. We conclude that the CD34 cell dose has an impact on the outcome of HSCT from sibling donor PBSCs.

X-Linked Thrombocytopenia and Thrombocytopathia: Attenuated Wiskott-Aldrich Syndrome

Detailed studies on the rare disorder X-linked thrombocytopenia showed that it resembles the Wiskott-Aldrich syndrome (WAS) in inheritance, clinical bleeding tendency, platelet morphology, marked thrombocytopenia and microplatelets. The calculated platelet mass was 5% of normal. Functional and biochemical studies indicated qualitatively normal aggregation and release mechanisms, whereas a moderate storage pool defect was present. The classical platelet membrane glycoproteins and lymphocyte sialophorin (CD 43) were normal.

The reason for the bleeding tendency was concluded to be deficient hemostatic plug formation resulting from the low platelet mass and a moderate storage pool defect.

The only clear distinction from WAS was the normal immunofunctional tests, the moderate tendency to infections and the absence of eczema. We therefore consider the trait as an attenuated form of WAS. That women are affected may indicate a particular variant.

Is a Prolonged Bleeding Time Associated with an Increased Risk of Hemorrhage after Liver Biopsy?

Bleeding time determination is not advised as a general preoperative hemostasis screening test, but it might be useful in some patient groups. Patients referred for liver biopsy frequently have coagulation disturbances and are at risk of hemorrhage. In this prospective study 219 liver biopsies were carried out regardless of a prolonged bleeding time, but with minimum requirements for hemoglobin concentration, platelet count, and tests of the internal and external coagulation pathways. The bleeding time was prolonged in the case of 48 (22%) of the biopsies. Significant bleeding as defined by a hemoglobin decrease of ≥2.0 g/dl occurred in nine patients. Three of these patients were bone marrow transplanted. Patients with a prolonged bleeding time carried a five times higher risk of bleeding (odds ratio = 5.0; confidence interval = 1.1-21.8; p = 0.019). We conclude that the bleeding time may give additional information on the risk of bleeding in some patient groups undergoing liver biopsy.

Key individuals for discerning pedigrees belonging to the same autosomal kinship class

The existence of pedigrees belonging to the same kinship class (i.e. indistinguishable through independent markers) is well known in the forensic community, and theoretical frameworks for autosomal and X-chromosomal markers were already developed for a pair of individuals. Nevertheless, studies for the cases where a greater number of individuals is available for testing are still lacking. With this work, we intend to pave the way for a theoretical and general framework, identifying the individuals/relatives that should be chosen to distinguish autosomal analyses between such pedigrees. In this work we identify the individuals/relatives that are non-informative for calculations (the pedigrees under discussion remaining indistinguishable independently of their genetic profile), as well as those that will likely be very informative, influencing the statistical outcome. For example, given the respective genotypes, to compare the likelihoods of the father of the individual B to be: (a.) the father, or (b.) a full-brother, of the individual A, the hypotheses H₁: "The individual A is paternal half-sibling of the individual B", and H₀: "The individual A is paternal uncle/aunt of the individual B" are considered. It is proved that considering just individuals A and B the hypotheses are equally likely. In this work we show that the same is also true for the case where the mother of B is available for testing, notwithstanding the hypotheses being differently weighted if the mother of A is considered. Similar considerations are done for other kinship hypotheses and/or individuals/relatives. Irrelevance of the genetic profile of some specific relatives are mathematically demonstrated, and data obtained from 20,000 simulated families are presented for the other cases.

Characterization of degradation and heterozygote balance by simulation of the forensic DNA analysis process

Simulation experiments were used to show the impact of varying extraction efficiency, aliquot proportion, and PCR efficiency on the heterozygote balance of a range of diploid and haploid cells. Reducing either parameters introduces variance. It is well-known that the variance in heterozygote balance increases as the amount of DNA is reduced. Surprisingly the distribution is in fact diamond shaped — the variance start to decrease at very low amounts of DNA. Simulations suggest that pristine diluted DNA is an acceptable approximation in validations to infer heterozygote balance. However, the difference in distribution of the variance between diploid and haploid cell types may, under some circumstances, need to be considered in statistical models. Finally, we exemplify how simulations can be used to predict the outcome of PCR for degraded samples. Visualizing the predicted DNA profile as an electropherogram can help to identify the best approach for sample processing.

Locomotion skills in adults with cerebral palsy

Objectives: To investigate self-reported locomotion skills in persons with cerebral palsy (CP) and to investigate variables potentially associated with deterioration of walking skills.

Design: Cross-sectional retrospective survey.

Setting and subjects: A multidimensional mailed questionnaire was sent to 766 persons with CP, 18 years or over, without intellectual disabilities, living in Norway.

Main outcome measures: The questionnaire consisted of demographic and diagnostic items, items on locomotion skills, and physical function (SF-36).

Results: In total 406 persons, 51% males and 49% females from 18 to 72 years (mean 34 years, SD 11 years) with all categories of CP responded. Median age for reported walking debut was 3 years, with a range from 1 to 14 years. In total 216 respondents (53%) walked without support, 104 persons (25%) walked with support, 39 persons (10%) had lost their walking skills, and 47 (12%) had never been able to walk. Mean level of physical function (SF-36) was 53 out of 100. There were 97 persons (27%) who reported improvement of walking skills, mainly before 25 years, 102 (28%) reported no change, and 160 (44%) reported deterioration, mainly before 35 years of age. Deterioration was significantly associated with older age, delayed walking debut and severe neurological impairment. Self-reported causes of deterioration were pain, fatigue and lack of adapted physical activity.

Conclusion: Deterioration of locomotion skills is a significant problem in persons with CP from an early age, documenting the need for life-long follow-up. The predictors above should be investigated in further clinical studies, searching for potential causal pathways.

Lipoprotein subfractions by nuclear magnetic resonance are associated with tumor characteristics in breast cancer

Background

High-Density Lipoprotein (HDL)-cholesterol, has been associated with breast cancer development, but the association is under debate, and whether lipoprotein subfractions is associated with breast tumor characteristics remains unclear.

Methods

Among 56 women with newly diagnosed invasive breast cancer stage I/II, aged 35–75 years, pre-surgery overnight fasting serum concentrations of lipids were assessed, and body mass index (BMI) was measured. All breast tumors were immunohistochemically examined in the surgical specimen. Serum metabolomics of lipoprotein subfractions and their contents of cholesterol, free cholesterol, phospholipids, apolipoprotein-A1 and apolipoprotein-A2, were assessed using nuclear magnetic resonance. Principal component analysis, partial least square analysis, and uni- and multivariable linear regression models were used to study whether lipoprotein subfractions were associated with breast cancer tumor characteristics.

Results

The breast cancer patients had following means: age at diagnosis: 55.1 years; BMI: 25.1 kg/m²; total-Cholesterol: 5.74 mmol/L; HDL-Cholesterol: 1.78 mmol/L; Low-Density Lipoprotein (LDL)-Cholesterol: 3.45 mmol/L; triglycerides: 1.18 mmol/L. The mean tumor size was 16.4 mm, and the mean Ki67 hotspot index was 26.5 %. Most (93 %) of the patients had estrogen receptor (ER) positive tumors (≥1 % ER+), and 82 % had progesterone receptor (PgR) positive tumors (≥10 % PgR+). Several HDL subfraction contents were strongly associated with PgR expression: Apolipoprotein-A1 (β 0.46, CI 0.22–0.69, p < 0.001), HDL cholesterol (β 0.95, CI 0.51–1.39, p < 0.001), HDL free cholesterol (β 2.88, CI 1.28–4.48, p = 0.001), HDL phospholipids (β 0.70, CI 0.36–1.04, p < 0.001). Similar results were observed for the subfractions of HDL1-3. We observed inverse associations between HDL phospholipids and Ki67 (β -0.25, p = 0.008), and in particular between HDL1’s contents of cholesterol, phospholipids, apolipoprotein-A1, apolipoprotein-A2 and Ki67. No association was observed between lipoproteins and ER expression.

Conclusion

Our findings hypothesize associations between different lipoprotein subfractions, and PgR expression, and Ki 67 % in breast tumors. These findings may have clinical implications, but require confirmation in larger studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12944-016-0225-4) contains supplementary material, which is available to authorized users.

On the use of dense SNP marker data for the identification of distant relative pairs

There has been recent interest in the exploitation of readily available dense genome scan marker data for the identification of relatives. However, there are conflicting findings on how informative these data are in practical situations and, in particular, sets of thinned markers are often used with no concrete justification for the chosen spacing. We explore the potential usefulness of dense single nucleotide polymorphism (SNP) arrays for this application with a focus on inferring distant relative pairs. We distinguish between relationship estimation, as defined by a pedigree connecting the two individuals of interest, and estimation of general relatedness as would be provided by a kinship coefficient or a coefficient of relatedness. Since our primary interest is in the former case, we adopt a pedigree likelihood approach. We consider the effect of additional SNPs and data on an additional typed relative, together with choice of that relative, on relationship inference. We also consider the effect of linkage disequilibrium. When overall relatedness, rather than the specific relationship, would suffice, we propose an approximate approach that is easy to implement and appears to compete well with a popular moment-based estimator and a recent maximum likelihood approach based on chromosomal sharing. We conclude that denser marker data are more informative for distant relatives. However, linkage disequilibrium cannot be ignored and will be the main limiting factor for applications to real data.

Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development

The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with the ability to multiplex several loci together. Use of the polymerase chain reaction (PCR) increased the sensitivity of the method to enable the analysis of a handful of cells. The first multiplexes were simple: 'the quad', introduced by the defunct UK Forensic Science Service (FSS) in 1994, rapidly followed by a more discriminating 'six-plex' (Second Generation Multiplex) in 1995 that was used to create the world's first national DNA database. The success of the database rapidly outgrew the functionality of the original system - by the year 2000 a new multiplex of ten-loci was introduced to reduce the chance of adventitious matches. The technology was adopted world-wide, albeit with different loci. The political requirement to introduce pan-European databases encouraged standardisation - the development of European Standard Set (ESS) of markers comprising twelve-loci is the latest iteration. Although development has been impressive, the methods used to interpret evidence have lagged behind. For example, the theory to interpret complex DNA profiles (low-level mixtures), had been developed fifteen years ago, but only in the past year or so, are the concepts starting to be widely adopted. A plethora of different models (some commercial and others non-commercial) have appeared. This has led to a confusing 'debate' about the 'best' to use. The different models available are described along with their advantages and disadvantages. A section discusses the development of national DNA databases, along with details of an associated controversy to estimate the strength of evidence of matches. Current methodology is limited to searches of complete profiles - another example where the interpretation of matches has not kept pace with development of theory. STRs have also transformed the area of Disaster Victim Identification (DVI) which frequently requires kinship analysis. However, genotyping efficiency is complicated by complex, degraded DNA profiles. Finally, there is now a detailed understanding of the causes of stochastic effects that cause DNA profiles to exhibit the phenomena of drop-out and drop-in, along with artefacts such as stutters. The phenomena discussed include: heterozygote balance; stutter; degradation; the effect of decreasing quantities of DNA; the dilution effect.

High-density lipoprotein-cholesterol, daily estradiol and progesterone, and mammographic density phenotypes in premenopausal women

High-density lipoprotein-cholesterol (HDL-C) may influence the proliferation of breast tumor cells, but it is unclear whether low HDL-C levels, alone or in combination with cyclic estrogen and progesterone, are associated with mammographic density, a strong predictor of breast cancer development. Fasting morning serum concentrations of HDL-C were assessed in 202 premenopausal women, 25 to 35 years of age, participating in the Norwegian Energy Balance and Breast Cancer Aspects (EBBA) I study. Estrogen and progesterone were measured both in serum, and daily in saliva, throughout an entire menstrual cycle. Absolute and percent mammographic density was assessed by a computer-assisted method (Madena), from digitized mammograms (days 7-12). Multivariable models were used to study the associations between HDL-C, estrogen and progesterone, and mammographic density phenotypes. We observed a positive association between HDL-C and percent mammographic density after adjustments (P = 0.030). When combining HDL-C, estradiol, and progesterone, we observed among women with low HDL-C (<1.39 mmol/L), a linear association between salivary 17β-estradiol, progesterone, and percent and absolute mammographic density. Furthermore, in women with low HDL-C, each one SD increase of salivary mid-menstrual 17β-estradiol was associated with an OR of 4.12 (95% confidence intervals; CI, 1.30-13.0) of having above-median percent (28.5%), and an OR of 2.5 (95% CI, 1.13-5.50) of having above-median absolute mammographic density (32.4 cm(2)). On the basis of plausible biologic mechanisms linking HDL-C to breast cancer development, our findings suggest a role of HDL-C, alone or in combination with estrogen, in breast cancer development. However, our small hypothesis generating study requires confirmation in larger studies.

A parametric approach to kinship hypothesis testing using identity-by-descent parameters

There is a large number of applications where family relationships need to be determined from DNA data. In forensic science, competing ideas are in general verbally formulated as the two hypotheses of a test. For the most common paternity case, the null hypothesis states that the alleged father is the true father against the alternative hypothesis that the father is an unrelated man. A likelihood ratio is calculated to summarize the evidence. We propose an alternative framework whereby a model and the hypotheses are formulated in terms of parameters representing identity-by-descent probabilities. There are several advantages to this approach. Firstly, the alternative hypothesis can be completely general. Specifically, the alternative does not need to specify an unrelated man. Secondly, the parametric formulation corresponds to the approach used in most other applications of statistical hypothesis testing and so there is a large theory of classical statistics that can be applied. Theoretical properties of the test statistic under the null hypothesis are studied. An extension to trios of individuals has been carried out. The methods are exemplified using simulations and a real dataset of 27 Spanish Romani individuals.

Gene variations in oestrogen pathways, CYP19A1, daily 17β-estradiol and mammographic density phenotypes in premenopausal women

INTRODUCTION

High mammographic density is an established breast cancer risk factor, and circulating oestrogen influences oestrogen-regulating gene expression in breast cancer development. However, less is known about the interrelationships of common variants in the CYP19A1 gene, daily levels of oestrogens, mammographic density phenotypes and body mass index (BMI) in premenopausal women.

METHODS

Based on plausible biological mechanisms related to the oestrogen pathway, we investigated the association of single nucleotide polymorphisms (SNPs) in CYP19A1, 17β-estradiol and mammographic density in 202 premenopausal women. DNA was genotyped using the Illumina Golden Gate platform. Daily salivary 17β-estradiol concentrations were measured throughout an entire menstrual cycle. Mammographic density phenotypes were assessed using a computer-assisted method (Madena). We determined associations using multivariable linear and logistic regression models.

RESULTS

The minor alleles of rs749292 were positively (P = 0.026), and the minor alleles of rs7172156 were inversely (P = 0.002) associated with daily 17β-estradiol. We observed an 87% lower level of daily 17β-estradiol throughout a menstrual cycle in heavier women (BMI >23.6 kg/m(2)) of rs7172156 with minor genotype aa compared with major genotype AA. Furthermore, the rs749292 minor alleles were inversely associated with absolute mammographic density (P = 0.032). Lean women with rs749292 minor alleles had 70 to 80% lower risk for high absolute mammographic density (>32.4 cm(2)); Aa: odds ratio (OR) = 0.23 (95% CI 0.07 to 0.75). Lean women with rs7172156 minor homozygous genotype had OR 5.45 for high absolute mammographic density (aa: OR = 5.45 (95% CI 1.13 to 26.3)).

CONCLUSION

Our findings suggest that two SNPs in CYP19A1, rs749292 and rs7172156, are associated with both daily oestrogen levels and mammographic density phenotypes. BMI may modify these associations, but larger studies are needed.

Familias 3 - Extensions and new functionality

In relationship testing the aim is to determine the most probable pedigree structure given genetic marker data for a set of persons. Disaster Victim Identification (DVI) based on DNA data from presumed relatives of the missing persons can be considered to be a collection of relationship problems. Forensic calculations in investigative mode address questions like "How many markers and reference persons are needed?" Such questions can be answered by simulations. Mutations, deviations from Hardy-Weinberg Equilibrium (or more generally, accounting for population substructure) and silent alleles cannot be ignored when evaluating forensic evidence in case work. With the advent of new markers, so called microvariants have become more common. Previous mutation models are no longer appropriate and a new model is proposed. This paper describes methods designed to deal with DVI problems and a new simulation model to study distribution of likelihoods. There are softwares available, addressing similar problems. However, for some problems including DVI, we are not aware of freely available validated software. The Familias software has long been widely used by forensic laboratories worldwide to compute likelihoods in relationship scenarios, though previous versions have lacked desired functionality, such as the above mentioned. The extensions as well as some other novel features have been implemented in the new version, freely available at www.familias.no. The implementation and validation are briefly mentioned leaving complete details to Supplementary sections.

Regression models for DNA-mixtures

This paper deals with the statistical interpretation of DNA mixture evidence. The conventional methods used in forensic casework today use something like 16 STR-markers. Power can be increased by rather using SNP-markers. New statistical methods are then needed, and we present a regression framework. The basic idea is that the traditional forensic hypotheses, commonly denoted HD and HP, are replaced by parametric versions: a person contributes to a mixture if and only if the fraction he contributes is greater than 0. This contributed fraction is a parameter of the regression model. The regression model uses the peak heights directly and there is no need to specify or estimate the number of contributors to the mixture. Also, drop-in and drop-out pose no principal problems. Data from 25 controlled blinded experiments were used to test the model. The number of contributors varied between 2 and 5, and the fractions contributed ranged from 0.01 to 0.99. The fractions were accurately estimated by the regression analyses. There were no false positives (i.e., in no cases were non-contributors declared to contributors). Some false negatives occurred for fractions of 0.1 or lower. Simulations were performed to test the model further. The analyses show that useful estimates can be obtained from a relatively small number of SNP-markers. Reasonable results are achieved using 300 markers which is close to the 313 SNPs in the controlled experiment. Increasing the number of SNPs, the analyses demonstrate that individuals contributing as little as 1% can reliably be detected, which suggests that cases beyond the reach of conventional forensic methods today can be reported.

Exact computation of the distribution of likelihood ratios with forensic applications

If complex DNA profiles, conditioned on multiple individuals are evaluated, it may be difficult to assess the strength of the evidence based on the likelihood ratio. A likelihood ratio does not give information about the relative weights that are provided by separate contributors. Alternatively, the observed likelihood ratio can be evaluated with respect to the distribution of the likelihood ratio under the defense hypothesis. We present an efficient algorithm to compute an exact distribution of likelihood ratios that can be applied to any LR-based model. The distribution may have several applications, but is used here to compute a p-value that corresponds to the observed likelihood ratio. The p-value is the probability that a profile under the defense hypothesis, substituted for a questioned contributor e.g. suspect, would attain a likelihood ratio which is at least the same magnitude as that observed. The p-value can be thought of as a scaled version of the likelihood ratio, giving a quantitative measure of the strength of the evidence relative to the specified hypotheses and the model used for the analysis. The algorithm is demonstrated on examples based on real data. R code for the algorithm is freely available in the R package euroMix.

Abstract 1362: Dyslipidemia, excess weight and high mammographic density are associated with high levels of daily estrogen and progesterone

Background: Dyslipidemia, excess weight, and high mammographic density have independently been associated with breast cancer development. However, little is known regarding the combined effect of dyslipidemia, excess weight and mammographic density on cyclic variation in estrogen and progesterone.

Material and Methods: 202 premenopausal women (25-35 years) participated in the Norwegian EBBA-I study including clinical examinations, and fasting blood sampling. Computer-assisted percent mammographic density (Madena) was obtained from digitized mammograms taken at day 7-12 of menstrual cycle. Daily saliva samples were collected across an entire menstrual cycle, and concentrations of 17β-estradiol and progesterone were measured at the Reproductive Ecology Laboratory, Harvard University, USA. Uni and multivariable linear and logistic regression models were used to study the combined association of high-density lipoprotein cholesterol (HDL-C), body mass index (BMI) and mammographic density with daily concentrations of 17β-estradiol and progesterone.

Results: Among women with mean age of 30.7 years, mean percent mammographic density 29.8 %, mean BMI 24.4 kg/m2, mean total cholesterol 4.45 mmol/l, and mean HDL-C 1.54 mmol/l, we observed overall mean salivary 17β-estradiol 16.2 pmol/l and progesterone 129.3 pmol/l. We used median split and women characterized by lower than median HDL-C (≤ 1.51 mmol/l), higher than median BMI (&gt; 23.6 kg/m2), and higher than median percent mammographic density (&gt; 28.5 %) (unfavorable profile), had higher concentrations of both 17β-estradiol (p = 0.005) and progesterone (p = 0.016) across the entire menstrual cycle, compared with women characterized by higher HDL-C(&gt; 1.51 mmol/l), lower BMI (≤ 23.6 kg/m2) and lower percent mammographic density (≤ 28.5 %) (favorable profile). Comparing the profiles, women with an unfavorable profile had 46 % higher overall mean 17β-estradiol (17β-estradiol; 22.2 versus 15.9 pmol/l) and 48% higher overall mean progesterone (progesterone; 187.5 versus 126.1pmol/l). These factors also showed strong associations with differences in AUC (area under curve) of these sex steroid hormones across the entire menstrual cycle, reflecting cumulative exposure. Women characterized by unfavorable profile had 48 % higher AUC estradiol compared with women having favorable profile (AUCe, 387, 95 % confidence interval (CI) 244 - 531 versus 262, 95% CI 244 - 281). Furthermore, women with unfavorable profile had 47 % higher AUC progesterone than women with favorable profile (AUCp, 1929, 95 % CI 1125 - 2733 versus 1309, 95% CI 1211 -1408).

Conclusion: A combination of low HDL-C, excess weight, and high percent mammographic density, was strongly associated with higher daily levels of 17β-estradiol and progesterone, and could in part explain the association of these factors with increased risk of breast cancer development.

Citation Format: Vidar G. Flote, Hanne Frydenberg, Giske Ursin, Anita Iversen, Morten W. Fagerland, Peter T. Ellison, Erik A. Wist, Thore Egeland, Anne-Sofie Furberg, Inger Thune. Dyslipidemia, excess weight and high mammographic density are associated with high levels of daily estrogen and progesterone. . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1362. doi:10.1158/1538-7445.AM2013-1362

Evaluating methods to correct for population stratification when estimating paternity indexes

The statistical interpretation of the forensic genetic evidence requires the use of allelic frequency estimates in the reference population for the studied markers. Differences in the genetic make up of the populations can be reflected in statistically different allelic frequency distributions. One can easily figure out that collecting such information for any given population is not always possible. Therefore, alternative approaches are needed in these cases in order to compensate for the lack of information. A number of statistics have been proposed to control for population stratification in paternity testing and forensic casework, Fst correction being the only one recommended by the forensic community. In this study we aimed to evaluate the performance of Fst to correct for population stratification in forensics. By way of simulations, we first tested the dependence of Fst on the relative sizes of the sub-populations, and second, we measured the effect of the Fst corrections on the Paternity Index (PI) values compared to the ones obtained when using the local reference database. The results provide clear-cut evidence that (i) Fst values are strongly dependent on the sampling scheme, and therefore, for most situations it would be almost impossible to estimate real values of Fst; and (ii) Fst corrections might unfairly correct PI values for stratification, suggesting the use of local databases whenever possible to estimate the frequencies of genetic profiles and PI values.

Using object oriented bayesian networks to model linkage, linkage disequilibrium and mutations between STR markers

In a number of applications there is a need to determine the most likely pedigree for a group of persons based on genetic markers. Adequate models are needed to reach this goal. The markers used to perform the statistical calculations can be linked and there may also be linkage disequilibrium (LD) in the population. The purpose of this paper is to present a graphical Bayesian Network framework to deal with such data. Potential LD is normally ignored and it is important to verify that the resulting calculations are not biased. Even if linkage does not influence results for regular paternity cases, it may have substantial impact on likelihood ratios involving other, more extended pedigrees. Models for LD influence likelihoods for all pedigrees to some degree and an initial estimate of the impact of ignoring LD and/or linkage is desirable, going beyond mere rules of thumb based on marker distance. Furthermore, we show how one can readily include a mutation model in the Bayesian Network; extending other programs or formulas to include such models may require considerable amounts of work and will in many case not be practical. As an example, we consider the two STR markers vWa and D12S391. We estimate probabilities for population haplotypes to account for LD using a method based on data from trios, while an estimate for the degree of linkage is taken from the literature. The results show that accounting for haplotype frequencies is unnecessary in most cases for this specific pair of markers. When doing calculations on regular paternity cases, the markers can be considered statistically independent. In more complex cases of disputed relatedness, for instance cases involving siblings or so-called deficient cases, or when small differences in the LR matter, independence should not be assumed. (The networks are freely available at http://arken.umb.no/~dakl/BayesianNetworks.).

Ultra-short course sirolimus contributes to effective GVHD prophylaxis after reduced-intensity allogeneic hematopoietic cell transplantation

Reduced-intensity conditioning (RIC) allo-SCT is a potentially curative treatment approach for patients with relapsed Hodgkin's or non-Hodgkin's lymphoma. In the present study, 37 patients underwent RIC allo-SCT after induction treatment with EPOCH-F(R) using a novel form of dual-agent immunosuppression for GVHD prophylaxis with CsA and sirolimus. With a median follow-up of 28 months among survivors, the probability for OS at 3 and 5 years was 56%. Treatment-related mortality was 16% at day +100 and 30% after 1 year of transplant. Acute GVHD grades II-IV developed in 38% of patients, suggesting that the regimen consisting of CsA and an ultra-short course of sirolimus is effective in the prevention of acute GVHD.

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions

Next-generation sequencing (NGS) techniques have already shown their potential in the identification of mutations underlying rare inherited disorders. We report here the application of linkage analysis in combination with targeted DNA capture and NGS to a Norwegian family affected by an undiagnosed mental retardation disorder with an autosomal recessive inheritance pattern. Linkage analysis identified two loci on chromosomes 9 and 17 which were subject to target enrichment by hybridization to a custom microarray. NGS achieved 20-fold or greater sequence coverage of 83% of all protein-coding exons in the target regions. This led to the identification of compound heterozygous mutations in NAGLU, compatible with the diagnosis of Mucopolysaccharidosis IIIB (MPS IIIB or Sanfilippo Syndrome type B). This diagnosis was confirmed by demonstrating elevated levels of heparan sulphate in urine and low activity of α-N-acetyl-glucosaminidase in cultured fibroblasts. Our findings describe a mild form of MPS IIIB and illustrate the diagnostic potential of targeted NGS in Mendelian disease with unknown aetiology.

Using X-chromosomal markers in relationship testing: calculation of likelihood ratios taking both linkage and linkage disequilibrium into account

X-chromosomal markers in forensic genetics have become more widely used during recent years, particularly for relationship testing. Linkage and linkage disequilibrium (LD) must typically be accounted for when using close X-chromosomal markers. Thus, when producing the weight-of-evidence, given by a DNA-analysis with markers that are linked, the normally used product rule is invalid. Here we present an implementation of an efficient model for calculating likelihood ratios (LRs) with markers on the X-chromosome which are linked and in LD. Furthermore, the model was applied on several cases based on data from the eight X-chromosomal loci included in the Mentype(®) Argus X-8 (Biotype). Using a simulation approach we showed that the use of X-chromosome data can offer valuable information for choosing between the alternatives in each of the cases we studied, and that the LR can be high in several cases. We demonstrated that when linkage and LD were disregarded, as opposed to taken into account, the difference in calculated LRs could be considerable. When these differences were large, the estimated haplotype frequencies often had a strong impact and we present a method to estimate haplotype frequencies. Our conclusion is that linkage and LD should be accounted for when using the tested set of markers, and the used model is an efficient way of doing so.

FTO genotype and weight gain in obese and normal weight adults from a Norwegian population based cohort (the HUNT study)

The fat mass and obesity associated gene ( FTO) is associated with bodyweight and obesity. The aim of this study was to investigate if FTO genotype affects weight gain in adulthood. We investigated the weight development over a period of 11 years in a case-control study, consisting of 1,632 cases (BMI≥35 kg/m (2)) and 3,379 normal weight controls (BMI 20-24.9 kg/m (2)) from a Norwegian population based cohort, the HUNT study. Subjects were aged 20-80 at baseline, 25% men and 75% women. FTO genotype was assessed by genotyping of the SNP rs1421085. A strong association between FTO and obesity was found, consistent with an additive gene effect. Cases had an average weight gain of 11.1 kg, whereas controls had an average weight gain of 1.4 kg. Genotype was neither associated with weight gain in obese, nor controls. Cases had an average weight gain of 10.7 kg for individuals with zero risk alleles, 11.3 for one risk allele and 11.1 kg for two risk alleles. Controls had an average weight gain of 1.4 kg, 1.4 and 1.3 for the respective genotypes. In conclusion, FTO was associated with obesity, but not with weight gain in adults during 11 years of follow-up.

Unrelated hematopoietic stem cell donors as research subjects

Requests for participation of unrelated stem cell donors in research transplant protocols are becoming more frequent. World Marrow Donor Association calls on donor registries to participate in research activities. Here, we discuss various implications of research participation and make some recommendations as how to make this possible.

X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene

CONTEXT

X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism (AHCH) is known to be caused by coding mutations in the nuclear receptor subfamily 0, group B, member 1 (NR0B1) gene, encoding the transcriptional repressor dosage-sensitive sex-reversal adrenal hypoplasia critical region on the X chromosome protein 1 (DAX1).

OBJECTIVE/PATIENTS

Four males in a family were affected by AHCH. Our aim was to locate the genetic cause of their disease, knowing that they had no mutation in the obvious candidate gene, NR0B1.

DESIGN

Linkage analysis of the X chromosome and mutational screening of conserved noncoding regions upstream of NR0B1 were performed. To functionally characterize the genetic defect, studies of transcription and expression of DAX1 and steroidogenic factor 1 (SF-1) were done.

RESULTS

A 60 Mb inversion on the X chromosome with one of the inversion breakpoints located in a conserved noncoding region 4 kb upstream of NR0B1 was detected. The inversion causes relocation of a putative SF-1 binding site implicated in murine gonadal development. A reporter construct lacking this enhancer element upstream of NR0B1 was unresponsive to SF-1 transcriptional activation. Immunohistochemistry suggested that the inversion leads to SF-1 silencing in the patients' testes both in childhood and in adult life.

CONCLUSION

We report a noncoding mutation causing AHCH, an inversion resulting in a phenotype similar to what is caused by intragenic NR0B1 null mutations. The inversion seems to disrupt and/or relocate regulatory sites crucial in DAX1 expression.

A CLEC16A variant confers risk for juvenile idiopathic arthritis and anti-cyclic citrullinated peptide antibody negative rheumatoid arthritis

Objective

Variants in CLEC16A have conferred susceptibility to autoimmune diseases in genome-wide association studies. The present work aimed to investigate the locus' involvements in juvenile idiopathic arthritis (JIA) and further explore the association with rheumatoid arthritis (RA), type 1 diabetes (T1D) and Addison's disease (AD) in the Norwegian population.

Methods

Three single nucleotide polymorphisms (SNPs) were genotyped in patients with RA (n=809), JIA (n=509), T1D (n=1211) and AD (n=414) and in healthy controls (n=2149).

Results

All diseases were associated with CLEC16A, but with different SNPs. The intron 22 SNP, rs6498169, was associated with RA (p=0.006) and JIA (p=0.016) and the intron 19 SNPs, rs12708716/rs12917716, with T1D (p=1×10−5) and AD (p=2×10−4). The RA association was confined to the anti-cyclic citrullinated peptide antibody (anti-CCP) negative subgroup (p=2×10−4).

Conclusion

This is the first report of a CLEC16A association with JIA and a split of the RA association according to anti-CCP status. Different causative variants underlie the rheumatic versus the organ specific diseases.

Parental SCN1A mutation mosaicism in familial Dravet syndrome

Different SCN1A mutations are known to cause a variety of phenotypes, such as generalized epilepsy with febrile seizures plus (GEFS+), Dravet syndrome and familial hemiplegic migraine (FHM). In Dravet syndrome, most mutations are de novo and familial cases are rare. In this study, Dravet syndrome is observed in two maternal half sisters. They have healthy fathers and their common mother has never experienced seizures, but has a lifelong history of migraine. Direct sequencing of DNA extracted from blood revealed a heterozygous SCN1A nonsense mutation c.3985C>T in the sisters, but not in the mother. The mutation induces a premature stop codon and probably leads to a non-functional protein. Further examination of the mother's DNA showed that she has a mosaicism of the mutation. This report of parental SCN1A nonsense mutation mosaicism in familial Dravet syndrome suggests that mosaicism might be more common than previously suspected and emphasizes the importance of taking mosaicism into account in genetic counselling of Dravet syndrome and SCN1A mutations. Furthermore, whether the migraine of the mother could be influenced by her SCN1A mutation mosaicism is not known, but increased awareness of migraine in future studies of SCN1A related epilepsies could clarify this intriguing link between migraine and epilepsy.