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The subtypes of these samples were assigned using PAMR, and results were cross-validated extensively using supervised hierarchical clustering and PCA to ensure the re-assignments of these samples to subtypes are consistent with the previous prediction.
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The CN for each sample was assigned using CopyCaller™ software version 2.0 (Applied Biosystems), which uses relative quantitative analysis.
To examine this more directly, a N,C labeled TGF-β3H4 sample was prepared, and its backbone resonances were assigned using standard triple-resonance methodology.
Diagnoses were assigned using Research Diagnostic Criteria [ 38]. 60 ml of blood sample was taken from each individual for DNA analysis.
Alleles were assigned using GeneMapper Software v37 (Applied Biosystems).
Haplotypes were assigned using PHASE (version 2.1).
A small proportion of Swedish samples are unassigned using AIMs, whereas all are assigned using PCAIMs.
The samples were assigned to Borrelia species using restriction fragment length polymorphism as described previously [2].
All other samples were assigned to geographically close populations using AIMs.
Although the assignment success for the MS/HW samples were generally lower, more than 97% of the MS/HW samples were assigned with nearly 98% accuracy using oncor with probability cut-off value 0.7.
Samples were assigned to one of three groups using a simulated sample trait (referred to as "disease status"), with 50 samples corresponding to control status, 25 samples corresponding to moderate disease status, and 25 samples corresponding to severe disease status (Methods).
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