Methods and compositions for identifying presence or absence of hypermethylation or hypomethylation locus
Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.
1. A collection of amplification primer pairs for identifying the presence or absence of a hypermethylated locus or a hypomethylated locus prepared by a process comprising:
(a) selecting one or more genomic loci wherein each locus comprises three or more features selected from:
(i) a locus length of about 5000 contiguous base pairs, or less,
(ii) at least 5 CpG methylation sites,
(iii) a plurality of restriction endonuclease recognition sites wherein the mean, median or absolute distance between each restriction endonuclease recognition site on the locus is about 20 to about 125 base pairs, and each of the restriction endonuclease recognition sites is recognized by one or more methylation-sensitive restriction endonucleases,
(iv) at least 1 restriction endonuclease recognition site per 1000 base pairs, wherein the at least one restriction endonuclease recognition site can be specifically digested by a methylation-sensitive restriction endonuclease,
(v) a locus comprising a methylation status of 60% or more in a minority nucleic acid species,
(vi) a locus comprising a methylation status of 40% or less in a majority nucleic acid species, and
(vii) a locus comprising a difference in methylation status of 5% or more between a minority nucleic acid species and a majority nucleic acid species; and
(b) preparing a plurality of oligonucleotide primer pairs, wherein each primer of each primer pair hybridizes to a portion of a strand of the locus selected in (a) for which the primer pair is specific, whereby a collection of amplification primers is prepared,
wherein at least one of the amplification primers of each of the primer pairs comprises a non-native element, and
wherein the one or more genomic loci are on chromosome 13, 18, or 21, and
wherein the genomic loci comprise SEQ ID NO: 85.
2. The collection of amplification primer pairs of claim 1 , wherein genomic loci having feature (iv) are selected in (a).
3. The collection of amplification primer pairs of claim 1 , wherein the feature of (a)(i) is 500 contiguous nucleotides, or less.
4. The collection of amplification primer pairs of claim 1 , wherein the at least 5 CpG methylation sites of (a)(ii) are at least 9 CpG methylation sites.
5. The collection of amplification primer pairs of claim 1 , wherein the mean, median or absolute distance between each restriction endonuclease recognition site of (iii) is about 40 to about 100 base pairs.
6. The collection of amplification primer pairs of claim 1 , wherein the feature of (a)(iv) is at least 10 restriction endonuclease recognition sites per 1000 base pairs.
7. The collection of amplification primer pairs of claim 1 , wherein genomic loci having features (ii), (iii) and (iv) are selected in (a).
8. The collection of amplification primer pairs of claim 1 , wherein genomic loci having features (ii), (iii) and (vii) are selected in (a).
9. The collection of amplification primer pairs of claim 1 , wherein genomic loci having features (ii), (iv) and (vii) are selected in (a).
10. The collection of amplification primer pairs of claim 1 , wherein genomic loci having features (iii), (iv) and (vii) are selected in (a).
11. The collection of amplification primer pairs of claim 1 , wherein genomic loci having feature (i) are selected in (a).
12. The collection of amplification primer pairs of claim 1 , wherein genomic loci having feature (v) are selected in (a).
13. The collection of amplification primer pairs of claim 1 , wherein genomic loci having feature (vi) are selected in (a).