Minimal Marker Set Research Articles

Serum histone H3 levels and platelet counts are potential markers for coagulopathy with high risk of death in septic patients: a single-center observational study

BackgroundRecent studies have suggested that anticoagulant therapy does not confer a survival benefit overall in sepsis, but might be beneficial in sepsis-associated disseminated intravascular coagulation (DIC). In particular, those with high Sequential Organ Failure Assessment (SOFA) scores might be the optimal target for anticoagulant therapy. However, both DIC and SOFA scores require the measurement of multiple markers. The purpose of this study was to explore a minimal marker set for determining coagulopathy at high risk of death in septic patients, wherein histone H3 levels were evaluated as indicators of both organ failure and coagulation activation.MethodsWe analyzed correlations among levels of serum histone H3 and other coagulation markers in 85 cases of sepsis using Spearman’s rank correlation test. We then compared the utility of histone H3 to that of other coagulation markers in predicting the traditional DIC state or 28-day mortality by receiver-operating characteristics analysis. Finally, we suggested cut-off values for determining coagulopathy with high risk of death, and evaluated their prognostic utility.ResultsSerum histone H3 levels significantly correlated with thrombin-antithrombin complex (TAT) levels (Spearman’s ρ = 0.46, p < 0.001), and weakly correlated with platelet counts (Spearman’s ρ = − 0.26, p < 0.05). Compared to other coagulation markers, histone H3 levels showed better performance in predicting 28-day mortality. When combining serum histone H3 levels with platelet counts, our new scoring system showed a concordance rate of 69% with the traditional four-factor criteria of DIC established by the Japanese Association for Acute Medicine. The 28-day mortality rates of the new and the traditional criteria-positive patients were 43% and 21%, respectively. Those of the new and the traditional criteria-negative patients were 5.7% and 9.4%, respectively.ConclusionsSerum histone H3 levels and platelet counts are potential markers for determining coagulopathy with high risk of death in septic patients. Further studies are needed to clarify the utility of serum histone H3 levels in the diagnostic of coagulopathy/DIC.

Distal upper limb kinematics during functional everyday tasks

Quantitative characterisation of upper limb motion allows the evaluation of the effect of pathology on functional task performance, potentially directing rehabilitation strategies. Movement patterns of the distal upper limb in healthy adults during functional tasks have not been extensively characterised. During five loaded functional tasks (drinking from a glass, pouring from a kettle, turning a handle, lifting a bag to a shelf, turning a key) the movement patterns were characterised using three-dimensional motion analysis with a minimal marker set in 16 healthy adults (10 M,6F, 27 (IQR:25–43)years). Joint angles reported include flexion/extension at the elbow and wrist, forearm supination/pronation and digits 2–5 metacarpophalangeal (MCP) joint flexion/extension. Additionally for the thumb the angle between the metacarpal of the thumb and the 2nd digit (Thumb base), the thumb MCP (Thumb MCP) and interphalangeal (Thumb IP) joint angles are presented. Durations of activities performed at self-selected comfortable speeds (3.36 (IQR:3.07,3.66)s turning a key to 6.20 (IQR:5.44,6.38)s drinking from a glass) are reported. The maximum joint angles used (median of participants’ maxima) were 141° of elbow flexion, 116° forearm supination, 36° wrist extension, 56° Thumb base, 14° Thumb MCP flexion, 18° Thumb IP flexion, 85° MCP2-5 flexion. The tasks of drinking from a glass, lifting a bag to a shelf and turning a key appeared to have the least variation in performance, suggesting that these activities are better suited to be selected as standardized tasks for assessing the impact of pathology on movement than pouring from a kettle and turning a handle.

A minimal markerset for three-dimensional foot function assessment: measuring navicular drop and drift under dynamic conditions

BackgroundThe validity of predicting foot pronation occurring mainly at the midfoot by surrogate measures from the rearfoot, like eversion excursion, is limited. The dynamic navicular mobility in terms of vertical navicular drop (dNDrop) and medial navicular drift (dNDrift) may be regarded as meaningful clinical indicators to represent overall foot function. This study aimed to develop a minimal approach to measure the two parameters and to examine their intra- and interday reliability during walking.MethodsThe minimal markerset uses markers at the lateral and medial caput of the 1st and 5th metatarsals, respectively, at the dorsal calcaneus and at the tuberosity of the navicular bone. Dynamic navicular drop and drift were assessed with three-dimensional motion capture in 21 healthy individuals using a single-examiner test-retest study design.ResultsIntra- and interday repeatability were 1.1 mm (ICC21 0.97) and 2.3 mm (ICC21 0.87) for dynamic navicular drop and 1.5 mm (ICC21 0.96) and 5.3 mm (ICC21 0.46) for dynamic navicular drift. The contribution of instrumental errors was estimated to 0.25 mm for dynamic navicular drop and 0.86 mm for dynamic navicular drift.ConclusionsInterday reliability was generally worse than intraday reliability primary due to day-to-day variations in movement patterns and the contribution of instrumental errors was below 23% for dynamic navicular drop but reached 57% for dynamic navicular drift. The minimal markerset allows to simply transfer the known concepts of navicular drop and drift from quasi-static clinical test conditions to functional tasks, which is recommended to more closely relate assessments to the functional behavior of the foot.

A practical clinical kinematic model for the upper limbs.

A novel clinically practical upper limb model is introduced that has been developed through clinical use in children and adults with neurological conditions to guide surgery to the elbow and wrist. This model has a minimal marker set, minimal virtual markers, and no functional joint centres to minimise the demands on the patient and duration of data collection. The model calculates forearm supination independently from the humerus segment, eliminating any errors introduced by poor modelling of the shoulder joint centre. Supination is calculated by defining the forearm segment twice, from the distal and proximal ends: first, using the ulna and radial wrist markers as a segment defining line and second using the medial and lateral elbow markers as a segment defining line. This is comparable to the clinical measurement of supination utilising a goniometer and enables a reduced marker set, with only the elbow, wrist, and hand markers to be applied when only the wrist and forearm angles are of interest. A sensitivity analysis of the calculated elbow flexion-extension angles to the position of the glenohumeral joint centre is performed on one healthy female subject, aged 20 years, during elbow flexion and a forward reaching task. A comparison of the supination angles calculated utilising the novel technique compared to the rotation between the humeral and forearm segments is also given. All angles are compared to a published kinematic model that follows the recommendations of the International Society of Biomechanics.

A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells.

Real-time, single-cell multiplex immunophenotyping of circulating tumor cells (CTCs) is hypothesized to inform diagnosis of tissue of origin in patients with carcinoma of unknown primary (CUP). In 20 to 50% of CUP patients, the primary site remains unidentified, presenting a challenge for clinicians in diagnosis and treatment. We developed a post-CellSearch CTC assay using multiplexed Q-dot or DyLight conjugated antibodies with the goal of detecting multiple markers in single cells within a CTC population. We adapted our approach to size-based CTC enrichment protocols for capturing CTCs and subsequent immunofluorescence (IF) using a minimal set of markers to predict the primary sites for common metastatic tumors. The carcinomas are characterized with cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA. IF has been optimized in cultured tumor cells with individual antibodies, then with conjugated antibodies to form a multiplex antibody set. With IF, we evaluated antibodies specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines and blood from metastatic prostate and breast cancer patients. This advanced technology provides a noninvasive, diagnostic blood test as an adjunct to routine tissue biopsy. Its further implementation requires prospective clinical testing.

Compensatory Versus Noncompensatory Shoulder Movements Used for Reaching in Stroke

Background. The extent to which the upper-limb flexor synergy constrains or compensates for arm motor impairment during reaching is controversial. This synergy can be quantified with a minimal marker set describing movements of the arm-plane. Objectives. To determine whether and how (a) upper-limb flexor synergy in patients with chronic stroke contributes to reaching movements to different arm workspace locations and (b) reaching deficits can be characterized by arm-plane motion. Methods. Sixteen post-stroke and 8 healthy control subjects made unrestrained reaching movements to targets located in ipsilateral, central, and contralateral arm workspaces. Arm-plane, arm, and trunk motion, and their temporal and spatial linkages were analyzed. Results. Individuals with moderate/severe stroke used greater arm-plane movement and compensatory trunk movement compared to those with mild stroke and control subjects. Arm-plane and trunk movements were more temporally coupled in stroke compared with controls. Reaching accuracy was related to different segment and joint combinations for each target and group: arm-plane movement in controls and mild stroke subjects, and trunk and elbow movements in moderate/severe stroke subjects. Arm-plane movement increased with time since stroke and when combined with trunk rotation, discriminated between different subject groups for reaching the central and contralateral targets. Trunk movement and arm-plane angle during target reaches predicted the subject group. Conclusions. The upper-limb flexor synergy was used adaptively for reaching accuracy by patients with mild, but not moderate/severe stroke. The flexor synergy, as parameterized by the amount of arm-plane motion, can be used by clinicians to identify levels of motor recovery in patients with stroke.

Abstract 1600: A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells

Abstract Abstract: Real-time, single-cell multiplex immunophenotyping of circulating tumor cells (CTCs) is hypothesized to inform diagnosis of tissue of origin in patients with carcinoma of unknown primary (CUP). In 20 to 50% of CUP patients, the primary site remains unidentified, presenting a challenge for clinicians in diagnosis and treatment. Invasive tissue biopsy is the gold standard for diagnosis but improved methodology is needed. We developed a post-CellSearch CTC assay using multiplexed Q-dot or DyLight conjugated antibodies with the goal of detecting multiple markers in single cells within a CTC population. We adapted our approach to size-based CTC enrichment protocols for capturing CTCs and subsequent immunofluorescence (IF) using a minimal set of markers to predict the primary sites for common metastatic tumors. The carcinomas are diagnosed with cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA) as the minimal set of informative markers. IF has been optimized in cultured tumor cells with individual antibodies, then with conjugated antibodies to form a multiplex antibody set. With IF, we evaluated antibodies specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines and blood samples from metastatic prostate and breast cancer patients. Our technological advance provides a noninvasive, inexpensive, diagnostic blood test as an adjunct to routine tissue biopsy. Its further implementation requires prospective clinical testing. Citation Format: Elizabeth M. Matthew, Lanlan Zhou, Namrata Vijayvergia, David T. Dicker, Karen S. Gustafson, Harry S. Cooper, Eric A. Ross, Bora Lim, Ramdane Harouaka, Si-Yang Zheng, Nicholas E. Lamparella, Joseph J. Drabick, Cristina I. Truica, Zhaohai Yang, Wafik S. El-Deiry. A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1600. doi:10.1158/1538-7445.AM2015-1600

Abstract 4822: Immunophenotyping circulating tumor cells in patients with unknown primary

Abstract Metastasis is responsible for the majority of cancer-related deaths. A limiting step in metastasis is access to circulation, thus circulating tumor cells (CTCs) should be present in all patients with metastatic tumors, which may have both diagnostic and prognostic value. Accounting for only 3-5%, carcinoma of unknown primary (CUP) presents a challenge for clinicians in diagnosis and therapy. In 20 to 50% of CUP patients, the primary remains undiagnosed even after a full diagnostic work up. Tissue biopsy is the standard for diagnosis but there is need for improved methodology, including a non-invasive blood test that relies on CTC analysis. Our overall objective is to utilize CTCs to provide insight into systemic cancer progression and approaches to therapy, including a CTC blood test as a tool for diagnosis, prognosis and therapy. We hypothesize that real-time, single-cell immunophenotype profiling of CTC populations will inform diagnosis of tissue of origin, reveal prognostic markers such as stem-like properties and predict tumor aggressiveness. We have been developing a post-Veridex CTC analysis method using multiplexed Q-dot conjugated antibodies with the goal of detecting multiple markers in each single cell within a CTC population to aid in CUP diagnosis including tissue of origin. We have adapted this method for use in CTCs captured using the flexible micro spring array (FMSA) size-based CTC enrichment protocol and other approaches for capturing and immunophenotyping live CTCs. Further adaptation of this protocol enables the use of Dye-Light conjugated primary antibodies. For carcinomas we use cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor (TTF-1), estrogen receptor (ER; for female patients) and prostate specific antigen (PSA; for male patients) as a minimal set of markers for the identification of lung, colon, prostate and breast cancer. Successful validation of antibodies to these five markers has enabled multiplexing after DyLight conjugation in positive and negative cell lines. This approach is currently being tested in CTCs from patients and is being expanded to understand the biology of CTCs through an evaluation of EMT and stem cell markers. Successful application of our CTC-CUP protocol to CTCs in patient samples is expected to provide a noninvasive, relatively quick and inexpensive blood test that can be both diagnostic and prognostic, which may be a valuable adjunct to routine biopsy. Circulating tumor cells may provide insight into the mechanism of systemic cancer progression, the characteristics of metastatic founder cells and changes within these cells as cancer progresses, thereby impacting the efficacy and evaluation of cancer therapy. Citation Format: Elizabeth M. Matthew, Lanlan Zhou, Bora Lim, Nicholas E. Lamparella, David T. Dicker, Jean-Nicolas Gallant, Monika Joshi, Sheldon L. Holder, Ramdane Harouaka, Siyang Zheng, Joseph J. Drabick, Cristina I. Truica, Zhaohai Yang, Wafik S. El-Deiry. Immunophenotyping circulating tumor cells in patients with unknown primary. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4822. doi:10.1158/1538-7445.AM2014-4822

Combinatorial approach to enumerate immunophenotypes in flow cytometry panels (TECH1P.872)

Abstract The identification of cell populations from flow cytometry has rarely been mapped in a multi-dimensional space. Instead, the focus is typically limited to a small number of pre-specified cell types already described in the literature. We propose to re-conceptualize the flow cytometry panel as a discovery tool to disentangle complex flow data into the simplest, most clinically relevant cell types. We present a combinatorial method to enumerate all possible immunophenotypes within a flow panel from a clinical trial study. We applied this approach to 11,000 raw flow cytometry files from a multi-panel flow experiment in a ragweed allergy clinical trial (ImmPort:SDY1), available from the publicly accessible, NIAID-funded Immunology Database and Analysis portal (ImmPort; immport.niaid.nih.gov). Files were processed through an automated pipeline that applied ImmPort’s FLOCK autogating tool to segregate cell populations based on the expression of individual surface markers. This yielded roughly 59,000 unique cell populations. Unsupervised hierarchical clustering revealed cell populations that were highly correlated with treatment conditions, based on the Pearson similarity measure. From these results we identified a subset of monocytes with positive expression for CD23 that were correlated with clinical outcome. We believe this approach can help identify the minimal set of markers needed to characterize functionally distinct cell populations associated with clinical outcome.

Robust Identification of Three-Dimensional Thumb and Index Finger Kinematics With a Minimal Set of Markers

This study presents a methodology to determine thumb and index finger kinematics while utilizing a minimal set of markers. The motion capture of skin-surface markers presents inherent challenges for the accurate and comprehensive measurement of digit kinematics. As such, it is desirable to utilize robust methods for assessing digit kinematics with fewer markers. The approach presented in this study involved coordinate system alignment, locating joint centers of rotation, and a solution model to estimate three-dimensional (3-D) digit kinematics. The solution model for each digit was based on assumptions of rigid-body interactions, specific degrees of freedom (DOFs) at each located joint, and the aligned coordinate system definitions. Techniques of inverse kinematics and optimization were applied to calculate the 3-D position and orientation of digit segments during pinching between the thumb and index finger. The 3-D joint center locations were reliably fitted with mean coefficients of variation below 5%. A parameterized form of the solution model yielded feasible solutions that met specified tolerance and convergence criteria for over 85% of the test points. The solution results were intuitive to the pinching function. The thumb was measured to be rotated about the CMC joint to bring it into opposition to the index finger and larger rotational excursions (&gt;10 deg) were observed in flexion/extension compared to abduction/adduction and axial rotation for all joints. While the solution model produced results similar to those computed from a full marker set, the model facilitated the usage of fewer markers, which inherently lessened the effects of passive motion error and reduced the post-experimental effort required for marker processing.

Phylomark, a Tool To Identify Conserved Phylogenetic Markers from Whole-Genome Alignments

The sequencing and analysis of multiple housekeeping genes has been routinely used to phylogenetically compare closely related bacterial isolates. Recent studies using whole-genome alignment (WGA) and phylogenetics from >100 Escherichia coli genomes has demonstrated that tree topologies from WGA and multilocus sequence typing (MLST) markers differ significantly. A nonrepresentative phylogeny can lead to incorrect conclusions regarding important evolutionary relationships. In this study, the Phylomark algorithm was developed to identify a minimal number of useful phylogenetic markers that recapitulate the WGA phylogeny. To test the algorithm, we used a set of diverse draft and complete E. coli genomes. The algorithm identified more than 100,000 potential markers of different fragment lengths (500 to 900 nucleotides). Three molecular markers were ultimately chosen to determine the phylogeny based on a low Robinson-Foulds (RF) distance compared to the WGA phylogeny. A phylogenetic analysis demonstrated that a more representative phylogeny was inferred for a concatenation of these markers compared to all other MLST schemes for E. coli. As a functional test of the algorithm, the three markers (genomic guided E. coli markers, or GIG-EM) were amplified and sequenced from a set of environmental E. coli strains (ECOR collection) and informatically extracted from a set of 78 diarrheagenic E. coli strains (DECA collection). In the instances of the 40-genome test set and the DECA collection, the GIG-EM system outperformed other E. coli MLST systems in terms of recapitulating the WGA phylogeny. This algorithm can be employed to determine the minimal marker set for any organism that has sufficient genome sequencing.

Abstract 3625: A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary (CUP) using circulating tumor cells

Abstract Metastasis is responsible for the majority of cancer-related deaths. A limiting step in metastasis is access to circulation, thus circulating tumor cells (CTCs) should be present in all patients with metastatic tumors, which may have both diagnostic and prognostic value. Accounting for only 2-3%, carcinoma of unknown primary (CUP) presents a challenge for clinicians in diagnosis and therapy. Tissue biopsy is the standard for diagnosis but there is need for improved methodology including a non-invasive blood test that may rely on CTC analysis. We have been developing a post-Veridex CTC analysis method using multiplexed Q-dot conjugated antibodies with the goal of detection of multiple markers in each single cell within a CTC population to aid in CUP diagnosis including tissue of origin. We have developed an immunofluorescence (IF) protocol with a minimal set of markers to predict the primary sites and provide prognostic information for common metastatic tumors: melanoma, lung, colorectal, upper gastrointestinal organs, and breast or prostate cancer. Two kits are available to isolate CTCs through Veridex CellSearch: melanoma kit (using melanoma antigen), and epithelial or carcinoma kit (using EpCam). A patient's blood is initially tested with both kits, and positive CTCs from the melanoma kit supports a diagnosis of melanoma, whereas positive CTCs from the epithelial kit supports carcinoma. For carcinomas, we use cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA) as the minimal set of markers. IF has been optimized in cultured tumor cells, first with individual antibodies, then quantum dots (Q-dot) conjugated multiplex quadra-antibody set. We evaluated antibodies by IF specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines. The CK7 and ER antibodies conjugated to Qdot 605 and 705 respectively demonstrated expression in the appropriate cell lines. CK7-Qdot 605 and ER-Qdot 705 expression in cells that were recovered after being spiked into normal blood samples and isolated by the Veridex CellSearch system was similar to that observed with unconjugated antibodies. Our data show that it is feasible to detect expression using Qdot-labeled multiplexed antibodies on tumor cells isolated from blood by Veridex CellSearch system. Successful application of this protocol to CTCs in patient samples is expected to provide a noninvasive, relatively quick and inexpensive blood test that can be both diagnostic and prognostic, which may be a valuable adjunct to routine biopsy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3625. doi:1538-7445.AM2012-3625

887 USING ARTIFICIAL INTELLIGENCE AND MACHINE-LEARNING ALGORITHMS WITH GENE EXPRESSION PROFILING TO PREDICT SUPERFICIAL BLADDER CANCER RECURRENCE AT INITIAL PRESENTATION

INTRODUCTION AND OBJECTIVES: 50%-70% of patients with superficial (Ta/T1, N0M0) bladder cancer (SBC) recur within 5 years of initial presentation. Tumor grade and multifocality are routinely used indicators of recurrence. SBCs’ propensity to recur persistently necessitates intense follow up and invasive treatment. It is therefore crucial to objectively determine SBCs’ recurrence potential to identify patients at greatest risk and minimize invasive follow up schedules for those harboring relatively indolent disease. This study used a machinelearning algorithm to identify SBC genes at initial presentation that were most predictive of recurrence, and used them in a molecular signature to predict recurrence risk within 5 years after TURBT. METHODS: Whole genome profiling was performed on 112 frozen SBCs obtained at first presentation by TURBT on Illumina Human WG-6 BeadChips. A genetic programming (GP) algorithm was used to evolve classifier mathematical models for outcome prediction. Cross-validation-based resampling and gene usage frequencies were used to identify the most prognostic genes, which were combined into rules used in a voting algorithm to predict a sample’s target class. Key genes were validated by quantitative PCR. RESULTS: 88 (79%) patients recurred within 5 years of initial presentation. A GP algorithm was used to select a minimal set of markers grouped as a classifier for predicting recurrence, and crossvalidation estimated its robustness by analyzing its ability to generalize to unseen samples. The classifier set included 21 genes that could predict recurrence. Quantitative PCR was done on a subset of 100 patients for these genes. With amplicon sizes limited to 100 bases and Ct values 35 not being considered, a 4-fold cross-validation (n 83) resulted in a 5-gene combined rule that incorporated a voting algorithm to yield 77% sensitivity and 85% specificity in predicting recurrence in the training set. The respective values in the test set were 69% and 62%. A singular 3-gene rule was also constructed that predicted recurrence with 80% sensitivity and 90% specificity in the training set. The respective values in the test set were 71% and 67%. CONCLUSIONS: Using primary SBCs from initial occurrences, GP identified transcripts in a reproducible fashion that were predictive of recurrence. These findings could potentially impact SBC management, including surveillance frequency, administration of adjuvant therapy, and selection of candidates for an expectant approach.

Minimal marker set for center of mass estimation in running

The purpose was to study the validity of a recently proposed method [Forsell C, Halvorsen K. A method for determining minimal sets of markers for the estimation of center of mass, linear and angular momentum. Journal of Biomechanics 2009;42(3):361–5] for estimating the trajectory of the whole-body center of mass (CoM) in the case of running at velocities ranging from 10 to 22 km h −1. The method gives an approximation to the CoM using the position of fewer markers on the body than the standard method of tracking each segment of the body. Fourteen male athletes participated. A standard method for determining the CoM from a model of 13 segments and using the position of 36 markers was used as reference method. Leave-one-out cross-validation revealed errors that decreased with increasing number of markers used in the approximative method. Starting from four markers, the error in absolute position of the CoM decreased from 15 mm to 3 mm in each direction. For the velocity of the CoM the estimation bias was neglectable, and the random error decreased from 0.15 to 0.05 m s −1. The inter-subject and intra-subject variability in the estimated model parameters increased with increasing number of markers. The method worked well also when applied to running at velocities outside the range of velocities in the data used to determine the model parameters. The results indicate that a model using 10 markers represents a good trade-off between simplicity and accuracy, but users must take into account requirements of their specific applications.

Proportioning Whole-Genome Single-Nucleotide–Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry

The identification of geographic population structure and genetic ancestry on the basis of a minimal set of genetic markers is desirable for a wide range of applications in medical and forensic sciences. However, the absence of sharp discontinuities in the neutral genetic diversity among human populations implies that, in practice, a large number of neutral markers will be required to identify the genetic ancestry of one individual. We showed that it is possible to reduce the amount of markers required for detecting continental population structure to only 10 single-nucleotide polymorphisms (SNPs), by applying a newly developed ascertainment algorithm to Affymetrix GeneChip Mapping 10K SNP array data that we obtained from samples of globally dispersed human individuals (the Y Chromosome Consortium panel). Furthermore, this set of SNPs was able to recover the genetic ancestry of individuals from all four continents represented in the original data set when applied to an independent, much larger, worldwide population data set (Centre d'Etude du Polymorphisme Humain-Human Genome Diversity Project Cell Line Panel). Finally, we provide evidence that the unusual patterns of genetic variation we observed at the respective genomic regions surrounding the five most informative SNPs is in agreement with local positive selection being the explanation for the striking SNP allele-frequency differences we found between continental groups of human populations.

An utter refutation of the ‘Fundamental Theorem of the HapMap’

The International HapMap Project was proposed in order to quantify linkage disequilibrium (LD) relationships among human DNA polymorphisms in an assortment of populations, in order to facilitate the process of selecting a minimal set of markers that could capture most of the signal from the untyped markers in a genome-wide association study. The central dogma can be summarized by the argument that if a marker is in tight LD with a polymorphism that directly impacts disease risk, as measured by the metric r(2), then one would be able to detect an association between the marker and disease with sample size that was increased by a factor of 1/r(2) over that needed to detect the effect of the functional variant directly. This "fundamental theorem" holds, however, only if one assumes that the LD between loci and the etiological effect of the functional variant are independent of each other, that they are statistically independent of all other etiological factors (in exposure and action), that sampling is prospective, and that the estimates of r(2) are accurate. None of these are standard operating assumptions, however. We describe the ramifications of these implicit assumptions, and provide simple examples in which the effects of a functional variant could be unequivocally detected if it were directly genotyped, even as markers in high LD with the functional variant would never show association with disease, even in infinite sample sizes. Both theoretical and empirical refutation of the central dogma of genome-wide association studies is thus presented.