A simple question about Affymetrix SNP platform

Question

[Na Sed]

In this paper , section "Affymetrix platform", the below paragraph has been written:

Affymetrix was the first to commercially produce SNP arrays, nearly a decade ago. The HuSNP assay, initially prototyped in Wang et al. (15), was designed to genotype 1494 SNPs on one chip. Subsequent versions increased stepwise from 10 000 to 100 000 to 500 000, and finally to nearly one million SNPs in the current release. Every SNP site is interrogated by a set of probes that are each 25-nt long. A probe is designed to be complementary, or very nearly complementary, to a portion of the DNA sequence harboring the SNP site (Figure 2a). In the first few versions of the array, each SNP was interrogated by between 24 and 40 distinct probe sequences, forming a probe set. Within a set, each probe is associated with either allele A or allele B. Additionally, each probe is either a perfect match (PM; perfectly complementary to one of the target alleles), or a mismatch (MM; identical to a perfect match probe except that the center base is altered so as to be perfectly complementary to neither allele). The idea of the mismatch probe comes from mRNA expression arrays (16), and their purpose is to measure background noise. The scheme yields quartets comprised of four types of probes: PMA, MMA, PMB and MMB. The computational goal is to convert these 8–10 probe quartet intensity measures from raw array data into a genotype inference—AA, AB or BB.

In the last sentence, it has been written that "8–10 probe quartet". Why "8-10"?

Answer 1

[Jan Oosting]

For each of the types (PMA, MMA, PMB, MMB) there are upto 10 probes. (hence the 24-40 distinct probes earlier in the paragraph) The earlier SNP arrays also had shifting positions around the SNP if p is the basepair position of the SNP, then there were probes between p-12 and p+12, but also p-11 to p+13 and p-13 to p+11 (all 25 nucleotides long)

I don't have experience with the earliest type with 1500 SNPs, but IIRC the 10k SNP array had 5 probes for each type, each shifted by 1 position. ( p-14 to p+10, p-13 to p+11, p-12 to p+12, p-11 to p+13, p-10 to p+14) Later Chiptypes all have fewer probes per SNP, and at a certain time the MM probes were discarded alltogether