Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes

Abstract

Single-nucleotide extension is a widespread method for typing Y-chromosomal single-nucleotide polymorphisms. In our study, we validated a multiplex minisequencing assay in a reduced-volume and in a low-volume approach. A four-plex assay was performed in a 6-microL multiplex reaction in 96-well microtiter reaction plates, which can be directly used for capillary electrophoresis. In a second approach, a six-plex assay was performed on a chemically structured glass slide. Both techniques have proven to be highly sensitive as well as time- and cost-saving, which makes them a valuable option not only for forensic purposes but also for population genetic studies where large sample numbers have to be analyzed. In the present paper, both techniques are compared and applied to analyze a population sample from the area of Turku, Finland. The most common haplogroup was found to be N1c*, which is nearly absent in western and central European populations. Additionally, 11 short tandem repeat markers were analyzed to further discriminate Y-chromosomal lineages.

Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

“…Although the node that joins DE and CF is often referred to as CT (in the sense that it encompasses the whole of haplogroups C to T), and the clade that encompasses B, DE, and CF is often referred to as BT (in the sense that it encompasses the whole of haplogroups B to T), we are not in favor of these labels as they are inconsistent with the meanings of other two‐letter labels such as CF (referring to the joint root of C and F, not the range C to F) and LT (referring to the joint root of L and T, not the range L to T). Instead, we therefore prefer the more intuitive labels CDEF and BCDEF, respectively, as used in previous publications [Heinrich et al., ; Underhill and Kivisild, ; van Oven et al., ].…”

Associations between human genetic and craniometric differentiation across North Eurasia: The role of geographic scale

“…Distance from sphenomaxillare superior to the most inferior point of the foramen infraorbitale Subspinale-staphylion Distance between left and right palatomaxillare laterale Maximal distance between the lateral walls of the nasal cavity below crista conchalis immediately after piriform aperture margin but before hiatus maxillaris From the point where the pterygopalatine suture intersects with the margin of the vomer to the most distant point on the floor of the nasal cavity Maximal distance between the lateral walls of the nasal cavity below crista conchalis anterior to choanae but posterior to hiatus maxillaris Staphylion -hormion Martin 1928 Distance between the points of intersection of the pterygopalatine suture and crista conchalis cont. (Pakendorf et al 2003) 81 (Jin et al 2009) Chukchi 24 (Starikovskaya et al 1998) No data Druze 622 (Shlush 2008) 109 (Zalloua 2008) Eskimo (Siberian Yupik) 50 (Raff et al 2015) 33 (Lell et al 2002) Evenk 40 (Pakendorf et al 2003) 96 Finn 432 (Meinila 2001;Richards 1996) 316 (Lappalainen 2006;Heinrich 2009) Han (North Chinese) 322 (Jin et al 2009) 242 (Jin et al 2009) Italian 70 (Rienzo 1991) 347 (Coia 2013;Batini 2015) Japanese 211 (Jin et al 2009) 154 (Jin et al 2009) Karelian 303 (Lappalainen 2008) 202 (Lappalainen 2006(Lappalainen , 2008 Khanty 209 (Pimenoff et al 2006) 27 (Pimenoff et al 2006) Komi 214 (Osipova 2005) 153 (Mirabal 2009;Trofimova 2015) Latvian 299 (Pliss 2006) 159 (Pliss 2015) Mansi 95 (Pimenoff et al 2006) 25 (Pimenoff et al 2006) Mongol 95 (Jin et al 2009) 65 (Jin et al 2009) Mordovian 102…”

Preimplantation Genetic Testing: Current Status and Future Prospects

“…In PGD for sickle cell anemia, we perform multiplex PCR of single blastomeres followed by detection of β-globin (HBB) gene mutations by mini-sequencing, which is also known as single-base primer extension (Kobayashi et al, 1995;Heinrich et al, 2009). Sickle cell anemia is an autosomal recessive disorder caused by single-base mutation in codon 6 of HBB gene, that substitutes a thymine for adenine.…”