Making Sense out of Y Chromosome

Polymorphisms

Or why males are so complicated...

Thomas Krahn
 Human Y Chromosome Basics

Only in males (exceptions)

Inherited in strict paternal line

About 58 million bases long

Only ~27 Mbases sequenced

Highly repetitive

Contains pseudo autosomal regions

Largest palindromes in human genome

 Large Scale ChrY Changes
Insertions / Deletions
Whole chromosome duplications

Ring Y chromosomes

Inversions

Translocations / Fusion chromosomes

Peter H.Vogt: AZF deletions and Y

chromosomal haplogroups Hum.
Microscopic karyotype Reprod. 11 (4): 319-336. doi:
10.1093/humupd/dmi017

FISH with target specific fluorescent probes

Male infertility

Gender determination Turner Syndrome 45,XO:46,XY:46XX = 50:30:20

(Sports / Olympics)
Premi S, Srivastava J, Panneer G, Ali S, 2008
Startling Mosaicism of the Y-Chromosome and
Tandem Duplication of the SRY and DAZ Genes in
Patients with Turner Syndrome. PLoS ONE 3(11):
e3796. doi:10.1371/journal.pone.0003796
 Y Chromosome Repeats

Y-STR (DYS19, DYS385,

DYF399)
Mini satellites (MSY)
Inverted repeats
Palindromes
Multi palindromes
Parallel repeats (TSPY)
Y chromosomal variation tracks the
evolution of mating systems in
chimpanzee and bonobo.
Schaller F, Fernandes AM, Hodler C,
Mnch C, Pasantes JJ, Rietschel W,
Schempp W (2010) PLoS ONE 5(9): Peter H.Vogt: AZF deletions and Y chromosomal haplogroups
e12482. doi:10.1371/journal.pone.0012482 Hum. Reprod. 11 (4): 319-336. doi: 10.1093/humupd/dmi017
 Y-STR

Classical paternal line sibling test

Interesting for genealogists (surname correlation)

Isolation of a male profile from a mixed trace

No contamination problems with female lab personal

Ready made multiplex kits available

(Powerplex Y, Yfiler, Argus Y)

Number of markers not sufficient for genealogists

because they demand higher resolution

Adding More Markers to PPY
DYS426 and
DYS388 are
usually slow
mutators, but in
some haplogroups
they suddenly
increase mutation
frequency. They
have been in the
FTDNA database
right from the start
but they are absent
in the PPY kit.

PPY has some

gaps in JOE and
TMR. Just enough
to fill them with
DYS426 and
DYS388
 More single copy Y-STRs
Quick & easy to score
Not severely influenced by recombination

Easy and understandable comparisons for

genealogists
Plenty of Y-STRs published

Many of them have standardized

nomenclature (NIST)
FTDNA was always market leader with

number of Y-STR (12, 25, 37, 67 and 111

marker panel plus specialty Y-STR)
My goal was always to have ALL markers

that the competitors had so that FTDNA

customers could compare with all databases.
 Why So Many Y-STR?
Huge surname projects with 800+ family members
Find splits in closely related Y lines

Predict haplogroups from Y-STR haplotypes

Consistency checks across panels

Precisely map Y chromosome deletions

Special STRs: Multi Copy Y-STR

DYS725:
Difficult to interpret dinucleotide repeat
but just a few 100 bp next to DYS464
Good to verify unusual DYS464 results

DYF408:
188 bp segment doesn't
actually contain STR repeat units.
Good to calibrate molar equivalents

DYF397:
Asymmetric P1/P3 palindromic Y-STR
2 copies on P1 and 2 copies on P3
Good to distinguish different deletions / duplications

DYS385, DYS464, DYF399, DYS425, DYF408

DYS385 Kittler Protocol

Kittler R, Erler A, Brauer S, Stoneking M, Kayser M (2003) Apparent

intrachromosomal exchange on the human Y chromosome explained by
population history. Eur. J. Hum. Genet. 11(4): 304-14.
 Using Adjacent SNPs to Separate
Loci of Multicopy Y-STRs

Fluorescein

JOE

TAMRA

DYS464 Extended Test (DYS464X)

Using Adjacent SNPs to Separate
Loci of Multicopy Y-STRs
 Y hgrou p D YS 464
A 1 1 g -1 3 g -1 3 g -1 6 g
E 1 4 g - 1 5 .3 g - 1 7 g - 1 8 g
E3b1 1 4 g - 1 5 .3 g - 1 7 g - 1 8 g

Typing of
G 1 3 g -1 4 g -1 5 g -1 5 g
G2* 1 2 g -1 2 g -1 2 g -1 3 g
I 1 2 g -1 4 g -1 5 g -1 6 g

DYS464X I1 a
I1 a 3
1 2 g -1 4 g -1 4 g -1 6 g
1 2 g -1 2 g -1 4 g -1 4 g -1 5 g -1 6 g Other haplogroups have
I1 b 1 1 g -1 4 g -1 4 g -1 4 g only G-type alleles
I1 b 1 1 g -1 4 g -1 4 g -1 5 g
I1 b 2 a 1 1 g -1 4 g -1 4 g -1 5 g
I1 b 2 a 1 1 1 g -1 1 g -1 4 g -1 5 g
I1 c 1 4 g -1 5 g -1 5 g -1 6 g
J2 a 1 * 1 2 g -1 3 g -1 5 g -1 6 g -1 6 g -1 6 g
N 1 4 g - 1 4 .3 g
R1a1* 1 2 g -1 5 g -1 5 g -1 6 g
R1b 1 6 c -1 6 c -1 6 g -1 6 g
R1b 1 5 c -1 6 c
R1b 1 5 c -1 5 c -1 7 c -1 7 g
R1b 1 4 c -1 6 c -1 7 c -1 7 g
R1b 1 4 c -1 5 c -1 6 g -1 7 c
R1b 1 6 c -1 6 g
R1b 1 5 c -1 5 c -1 6 c -1 6 g
R1b 1 4 c -1 5 c -1 7 c -1 7 g R1b has usually 3 C-type
R1b 1 5 c -1 6 c -1 7 g -1 7 g
R1b 1 5 c -1 6 c alleles and one G-type allele
R1b 1 5 c -1 5 c -1 5 c -1 5 c
R1b 1 5 c -1 5 c -1 7 c -1 7 g
R1b 1 5 c -1 7 c -1 7 c -1 8 g
R1b 1 5 c -1 5 c -1 7 c -1 8 g
R1b 1 5 c -1 5 c -1 6 g -1 7 c
R1b 1 6 c -1 6 c -1 7 c -1 7 g
R1b 1 4 c -1 5 c -1 5 c -1 5 g
R1b 1 5 c -1 5 c -1 6 c -1 8 g
R1b 1 5 c -1 5 c - 1 6 c - 1 7 .1 g
R1b 1 5 c -1 5 c -1 6 g -1 7 c
R1b 1 3 c -1 5 c -1 7 c -1 7 g
R1b
R1b
1 5 c -1 5 c -1 7 g -1 7 g
1 5 c -1 6 c -1 6 c -1 8 g
Exceptions most likely
R1b 1 5 c -1 5 c -1 6 c -1 7 c products of recLOH
Palindromic Map
 RecLOH
centromere 9 39 14
DYF371 DYF399 DYS464
N.N. DYF397 DYF401 DYF387 DYS459 DYF385 DYS724 C-type DYF408 T-type C-type DYS725
188 bp
188 bp P1
N.N. DYF397 DYF401 DYF387 DYS459 DYF385 DYS724 DYF371 DYF408 DYF399 DYS464 DYS725
C-type C-type C-type
telomere
10 36 16

centromere 10
9 39
36 16
14
DYF371 DYF399 DYS464
N.N. DYF397 DYF401 DYF387 DYS459 DYF385 DYS724 C-type DYF408 T-type C-type DYS725
188 bp
188 bp P1
N.N. DYF397 DYF401 DYF387 DYS459 DYF385 DYS724 DYF371 DYF408 DYF399 DYS464 DYS725
C-type C-type C-type
telomere
10 36 16

Recombination driven Loss Of Heterozygosity

 P1/P2 Deletion Mechanism
Symmetry in the red/red (P1/P2) region allows for another
irregular conformation:
DYF397

P3
DYF397

DYF399 Recombination breakpoint

ins G DYF399
T-type DYS464 DYS725 DYS725 DYS464 C-type DYF408
188 bp

DYF399 DYS464G DYS725 DYS725 DYS464

T-type

DYF408
188 bp

N.N.

Circle conformation
DYF371 DYF397

DYS724 DYF385 DYF387 DYF401

 P1/P2 Deletion Mechanism
The circular DNA molecule can't replicate on its own and gets
lost in the next cell cycle
DYF397

P3
DYF397
DYF399
ins G
T-type DYS464 DYS725 DYS725 DYS464 DYF399 DYF408
188 bp

DYF399 DYS464G DYS725 DYS725 DYS464

T-type

DYF408 N.N.
188 bp

Deletion
DYF371 DYF397

DYS724 DYF385 DYS459 DYF387 DYF401

 Special Y-STRs: DYS389
DYS389 I+II fusion repeat observed

TCTG TCTA TCTG TCTA

SNPs are also affected by ChrY Self-
Recombination

L88 region in haplogroup J-L26/L27

SNPs are also affected by ChrY Self-
Recombination

L88 region in haplogroup E-M2

SNPs are also affected by ChrY Self-
Recombination
ChrX
ChrY

L88

L88 region of highly similar ChrX sequence

 Y-SNPs and Haplogroups

Haplogroups are defined by

stable Y-SNPs
YCC haplogroup tree

(most parsimonous tree)

Hundreds of refinements

and additions
The same characteristic

mutation often shows up in

completely distinct branches of
the tree (.2)
Parallel and back mutations happen

in real life
Those can often be explained

by recombination events
Keeping Track of New Y-SNPs and Y
Tree Changes

Ymap Y chromosome browser

contains information about most
published Y markers
Don't add new marker names

when they already exist

Info about location, base change,

primers, hg association and

palindrome position
Based on gbrowse

Instantly synchronized with

our LIMS db

Http://ymap.ftdna.com
Keeping Track of New Y-SNPs and Y
Tree Changes

Ytree (Draft Y chromosome tree)

Node based structure
http://ytree.ftdna.com
New SNPs found are instantly added

Automatically keeps a traceable change log

 Walk Through the Y Project
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A B C D E F G H I J K L M N O P Q R S T

Coverage (currently) ~ 200 kB Sanger sequences

On average 1.2 new SNPs per participant found
Verification and mapping of new mutations on Ytree

230 WTY participants from mainly European haplogroups

Designing PCR Primers for ChrY
Segments Input
target location

fastacmd +/- 500 bp

preset P3 params.

BLAST vs. all

human chromosomes

Pick best 1000

hits (exclude identity)

fastacmd and
create mispr. lib

Primer3
Manually change
parameters

Good primers found?

no, maybe
yes
Output
prim. with M13
ChrY Self Homology
ChrY Similarity to Other
Chromosomes
 Design of a ChrY Library
Enrichment Micro-Array

NimbleGen Titanium Sequence Capture 385K Array

454 Sequencing of Enriched Y Libs
Nextera Lib >> Nimblegen Y enrichment >> 454

From 563 to 125602 unique ChrY matching reads per 1/8 region
 Next Gen ChrY Sequencing as a
Commercial Product?
To enrich or not enrich? (low cost vs. information gain)
Problem with short reads (assembly, wrong mapping)

Verification of new mutations by Sanger sequencing

What can a genealogist learn

from a huge package of
sequencing data? How can
we design comparison
databases with only partially
overlapping datasets
(sequencing gaps)?

Bringing all information from

STR, SNP, WTY, 454,
Axiom, Infinium etc. together