Population stratification—allele frequency differences between cases and controls due to systematic ancestry differences—can cause spurious associations in disease studies. We describe a method that enables explicit detection and correction of population stratification on a genome-wide scale. Our method uses principal components analysis to explicitly model ancestry differences between cases and controls. The resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers. Population stratification—allele frequency differences between cases and controls due to systematic ancestry differences—can cause spurious associations in disease studies 1‐8 . Because the effects of stratification vary in proportion to the number of samples 9 , stratification will be an increasing problem in the large-scale association studies of the future, which will analyze thousands of samples in an effort to detect common genetic variants of weak effect. The two prevailing methods for dealing with stratification are genomic control and structured association 9‐14 . Although genomic control and structured association have proven useful in a variety of contexts, they have limitations. Genomic control corrects for stratification by adjusting association statistics at each marker by a uniform overall inflation factor. However, some markers differ in their allele frequencies across ancestral populations more than others. Thus, the uniform adjustment applied by genomic control may be insufficient at markers having unusually strong differentiation across ancestral populations and may be superfluous at markers devoid of such differentiation, leading to a loss in power. Structured association uses a program such as STRUCTURE 15 to assign the samples to discrete subpopulation clusters and then aggregates evidence of association within each cluster. If fractional membership in more than one cluster is allowed, the method cannot currently be applied to genome-wide association studies because of its intensive computational cost on large data sets. Furthermore, assignments of individuals to clusters are highly sensitive to the number of clusters, which is not well defined 14,16 .

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Principal components analysis corrects for stratification in genome-wide association studies

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

/pdf/minimal-information-for-studies-of-extracellular-vesicles-3s0intarv4.pdf

Minimal information for studies of extracellular vesicles 2018 (MISEV2018) : a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The aim of this updated guideline is to provide comprehensive and timely evidence-based recommendations on the prevention of future stroke among survivors of ischemic stroke or transient ischemic attack. The guideline is addressed to all clinicians who manage secondary prevention for these patients. Evidence-based recommendations are provided for control of risk factors, intervention for vascular obstruction, antithrombotic therapy for cardioembolism, and antiplatelet therapy for noncardioembolic stroke. Recommendations are also provided for the prevention of recurrent stroke in a variety of specific circumstances, including aortic arch atherosclerosis, arterial dissection, patent foramen ovale, hyperhomocysteinemia, hypercoagulable states, antiphospholipid antibody syndrome, sickle cell disease, cerebral venous sinus thrombosis, and pregnancy. Special sections address use of antithrombotic and anticoagulation therapy after an intracranial hemorrhage and implementation of guidelines.

/pdf/guidelines-for-the-prevention-of-stroke-in-patients-with-4s66xf1dte.pdf

Guidelines for the prevention of stroke in patients with stroke and transient ischemic attack: a guideline for healthcare professionals from the American Heart Association/American Stroke Association

http://xoomer.virgilio.it/lusebra/NuoviFile/PrevenzioneTVP.pdf

Prevention of venous thromboembolism

Activated protein C (APC) is a serine protease with potent anticoagulant properties, which is formed in blood on the endothelium from an inactive precursor During normal haemostasis, APC limits clot formation by proteolytic inactivation of factors Va and VIIIa (ref 2) To do this efficiently the enzyme needs a nonenzymatic cofactor, protein S (ref 3) Recently it was found that the anticoagulant response to APC (APC resistance) was very weak in the plasma of 21% of unselected consecutive patients with thrombosis and about 50% of selected patients with a personal or family history of thrombosis; moreover, 5% of healthy individuals show APC resistance, which is associated with a sevenfold increase in the risk for deep vein thrombosis Here we demonstrate that the phenotype of APC resistance is associated with heterozygosity or homozygosity for a single point mutation in the factor V gene (at nucleotide position 1,691, G-->A substitution) which predicts the synthesis of a factor V molecule (FV Q506, or FV Leiden) that is not properly inactivated by APC The allelic frequency of the mutation in the Dutch population is approximately 2% and is at least tenfold higher than that of all other known genetic risk factors for thrombosis (protein C (ref 8), protein S (ref 9), antithrombin10 deficiency) together

/pdf/mutation-in-blood-coagulation-factor-v-associated-with-33avp1ullq.pdf

Mutation in blood coagulation factor V associated with resistance to activated protein C

https://scholarlypublications.universiteitleiden.nl/access/item%3A3138188/view

A common genetic variation in the 3'-untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increase in venous thrombosis.

https://scholarlypublications.universiteitleiden.nl/access/item%3A3137456/view

Venous thrombosis due to poor anticoagulant response to activated protein C: Leiden Thrombophilia Study

https://scholarlypublications.universiteitleiden.nl/access/item%3A3138603/view

Increased risk of venous thrombosis in oral-contraceptive users who are carriers of factor v leiden mutation

Background Factor XI, a component of the intrinsic pathway of coagulation, contributes to the generation of thrombin, which is involved in both the formation of fibrin and protection against fibrinolysis. A deficiency of factor XI is associated with bleeding, but a role of high factor XI levels in thrombosis has not been investigated. Methods We determined factor XI antigen levels in the patients enrolled in the Leiden Thrombophilia Study, a large population-based, case–control study (with a total of 474 patients and 474 controls) designed to estimate the contributions of genetic and acquired factors to the risk of deep venous thrombosis. Odds ratios were calculated as a measure of relative risk. Results The age- and sex-adjusted odds ratio for deep venous thrombosis in subjects who had factor XI levels above the 90th percentile, as compared with those who had factor XI levels at or below that value, was 2.2 (95 percent confidence interval, 1.5 to 3.2). There was a dose–response relation between the facto...

https://www.nejm.org/doi/pdf/10.1056/NEJM200003093421004

Rogier M. Bertina

Papers

Mutation in blood coagulation factor V associated with resistance to activated protein C

A common genetic variation in the 3'-untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increase in venous thrombosis.

Venous thrombosis due to poor anticoagulant response to activated protein C: Leiden Thrombophilia Study

Increased risk of venous thrombosis in oral-contraceptive users who are carriers of factor v leiden mutation

High levels of coagulation factor XI as a risk factor for venous thrombosis.