For this reason, we defined them as hotspot SNPs which covered all 10 cancer types included in this study (Table 3).>> -wrap-foot> wildtype/wildype/wild type, indicating wild genotype; wt/var, wild type/variant type, indicating heterozygote; var/var, variant type/variant type, indicating variant genotype; HWE, Hardy-Weinberg equilibrium.
In the 103 cases of ALCL, 62 (60%) were ALK positive, and either showed both cytoplasmic and nuclear staining indicative of the presence of NPM-ALK [49 cases, 79%,, or cytoplasmic staining only indicating variant-ALK fusions 13 cases, 21%,.
Large clinico-pathologic studies of ALCL have shown that about 80% of cases of ALK + ALCL exhibit cytoplasmic and nuclear staining indicative of the presence of NPM-ALK; whereas the remaining 20% express ALK proteins only in the cytoplasm of the tumor cells, indicating variant-ALK fusions [ 1, 13, 25].
"A" indicates wild allele, and "a" indicates variant allele.
Where the letters are duplicated, the upper letter(s) indicate wild type and the lower letter(s) indicate variant sequences.
Transcripts from H. sapiens indicate variant forms at the N-terminal end, which lack the TM domain.
Code H-Ax indicates no variant nucleotides in SC, variant in J5; Code H-Bx indicates variant nucleotides in SC, no variant in J5; Code AH-x indicates asymmetric variation in both SC and J5.
Comparative genomic analysis of the IL4I1_2 variant was done with help of the UCSC genome browser [ 53], which indicated variant cDNAs from mouse [ 58] (ESTs Acc BY100275, BY099330, BY087056, BY092834, BY088421) and rat (Acc CV117152).
M1: Aa vs. AA, heterozygote comparison; M2: aa vs. AA, homozygote comparison; M3: Aa + aa vs. AA, dominant model; M4: aa vs. AA + Aa, recessive model; M5: a vs. A, allelic model (A indicates wild allele, a indicates variant allele).
Cells expressing indicated variant Beclin 1 were suspended in (150 mM NaCl, 10 mM HEPES (pH 7.4), 10 mM mannitol, 50 mM sucrose, 1 mM EDTA, 1 mM EGTA, 1 mM PMSF) and homogenized by Dounce homogenizer.
Asterisk is used to indicate variants which are geographically assigned.
