1. Haplotype Counting for Sensitive Chimerism Testing
Marija Debeljak, Evelina Mocci, Max C. Morrison, Aparna Pallavajjalla, Katie Beierl, Marie Amiel, Michaël Noë, Laura D. Wood, Ming- Tseh Lin, Christopher D. Gocke, Alison P. Klein, Ephraim J. Fuchs, Richard J. Jones, James R. Eshleman 
The Journal of Molecular Diagnostics 
Volume 19, Issue 3, Pages (May 2017)
DOI: /j.jmoldx
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Haplotype counting approach. A: Shown are theoretical haplotypes (horizontal bars) containing four single-nucleotide polymorphisms (SNPs), where pretransplant analysis shows a donor (left) is homozygous for haplotype number 1 (AACC) and recipient (right) who is homozygous for haplotype number 2 (CCTT). B: Post-transplant sample where 100,000 reads (blue bar) perfectly match the donor (haplotype number 1), 100 reads with guanine at the third SNP position, and 100 reads with cytosine at the first SNP position (green bars). The 200 reads with a single base change can be attributed to PCR error because they do not perfectly match either donor or recipient haplotypes. As such, this sample would be interpreted as 100% donor. C: Another post-transplant sample that contains 99,000 reads (blue bar) that perfectly match the donor haplotype, and 1000 reads (red bar) that perfectly match the recipient haplotype, and so are interpreted as real. The 100 reads (green bar) with a single cytosine are PCR errors because they cannot be attributed to either donor or recipient haplotype. Accordingly, this sample would be interpreted as containing 1% recipient DNA.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3. Figure 2
Overall strategy. Previously, using the 1000 Genomes data and a window of 300 bp that contained at least nine single-nucleotide polymorphisms (SNPs), we identified 4349 polymorphic loci (dashed box).12 Polymorphisms at the eight selected loci were confirmed in eight whole genome sequencing (WGS) normal samples. Primers and polymorphism were initially confirmed by PCR and Sanger sequencing. Total of 45 individuals from three populations (15 individuals each) were PCR amplified and sequenced. Using sequenced data in a blind manner (M.D. and E.M.), we identified 30/30 sequenced samples, and none of the 15 control samples. NGS, next-generation sequencing.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4. Figure 3
Polymorphic region of the FARP1 locus. A: Shown are nine different haplotypes observed in FARP1 locus. Only single-nucleotide polymorphisms (SNPs) that differ from reference haplotype (FARP1-1) are shown (red, boldfaced). B: Number of SNP differences between FARP1 haplotypes. Some haplotype combinations are more informative, such as FARP1-5 and FARP1-6 or FARP1-3 and FARP1-7 (boxes). Others have fewer discriminating SNPs, such as FARP1-1 and FARP1-2 or FARP1-2 and FARP1-7 (dashed boxes). C: Intron 19 of FARP1 (blue line) containing 12 SNPs (red Xs) and two FARP1 PCR primers (yellow). The PCR primers are tailed on their 5′ ends with sequencing adaptors (orange).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

5. Figure 4
Host DNA detected in a series of nonrelapse and before relapse bone marrow samples. Using the nonrelapse samples, a threshold of (mean plus 3 SDs) was generated. Samples from recipients who subsequently relapsed were significantly higher. Horizontal bars indicate median values (nonrelapse median, 0.020% recipient; relapse median, 0.24% recipient). SEM was for nonrelapse group and for the relapse group. P value between the groups was (Mann-Whitney rank sum test).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions