Evidence for Genetic Linkage of Alzheimer's Disease to Chromosome 10q Lars Bertram, Deborah Blacker, Kristina Mullin, Devon Keeney, Jennifer Jones, Sanjay Basu, Stephen Yhu, Melvin G. McInnis, Rodney C. P. Go, Konstantinos Vekrellis, Dennis J. Selkoe, Aleister J. Saunders, and Rudolph E. Tanzi

The original sample included a total of 1500 subjects from 449 families with two or more affected subjects per family. Families in which any sampled individual had an onset age under 50 years were excluded (n = 14 families and 74 subjects), yielding 1426 individuals from 435 families for the present analyses. Over the ten years that the NIMH sample has been followed, a clinical diagnosis of AD has been confirmed at autopsy in 94% of the cases.

Markers were chosen according to maps from NCBI (http://www.ncbi.nlm.nih.gov/); LDB (http://cedar.genetics.soton.ac.uk/public_html/); Marshfield Center for Medical Genetics (http://research.marshfieldclinic.org/genetics/); GDB (http://gdbwww.gdb.org/gdb/). All marker locations in the text are expressed in Kosambi cM according to the genetic map from Marshfield.

APOE was genotyped as described previously (3). Marker loci (and their observed heterozygosity) included in the linkage analysis from p-ter to q-ter are as follows: D10S1225 (0.78), D10S564 (0.62), D10S583 (0.87), D10S1710 (0.60), D10S566 (0.65), D10S1671 (0.72) and D10S1741 (0.58). Marker genotypes were available on average for 82% of the sampled subjects. Primer sequences and PCR conditions were obtained from GDB, primer oligonucleotides were custom synthesized by Life Technologies (Rockville, MD). All PCR reactions were performed on ~ 30 ng of genomic DNA in a 10 ml reaction volume containing 3 pmol of each primer, 5 ml of Taq PCR Master Mix (Qiagen, Inc.) and 0.1 ml of [a-33P]dATP (1 uCi). After amplification, PCR products were denatured for 3 min at 94°C and then separated by polyacrylamide gel electrophoresis (6%, National Diagnostics, Atlanta, GA) for 1-3 h at 40-60 W and exposed to film for 24-48 h. All DNA samples are stored in a centralized cell repository at Rutgers University, New Brunswick, NJ.

Supplemental Table 1. Autosomal recessive model, maximum two-point parametric LOD scores (Zmax) and recombination fractions (R). Families were considered 'late-onset' if all sampled affecteds had onset ages 65 years. Marker locations in Kosambi cM according to the Marshfield map.
Marker (location)	All families Zmax (R)	Late-onset Zmax (R)
D10S1225 (80.8 cM)	0.4 (0.36)	0.9 (0.32)
D10S564 (112.6 cM)	0 (0.50)	0 (0.50)
D10S583 (115.3 cM)	2.7 (0.28)	2.4 (0.28)
D10S1710 (124.3 cM)	0.8 (0.32)	1.1 (0.30)
D10S566 (127.1 cM)	1.1 (0.32)	0.6 (0.34)
D10S1671 (127.1 cM)	2.9 (0.28)	3.8 (0.24)
D10S1741 (128.2 cM)	0.4 (0.35)	0.3 (0.36)

Supplemental Table 2. Autosomal dominant model, maximum two-point parametric LOD scores (Zmax) and recombination fractions (R). Families were considered 'APOE e4/4-positive' if at least one affected family-member carried the e4/4 genotype and 'APOE e4/4-negative' otherwise. Marker locations in Kosambi cM according to the Marshfield map.
Marker (location)	APOE e4/4-positive Zmax (R)	APOE e4/4-negative Zmax (R)
D10S1225 (80.8 cM)	0.1 (0.32)	0.4 (0.30)
D10S564 (112.6 cM)	0 (0.50)	0 (0.50)
D10S583 (115.3 cM)	1.2 (0.20)	2.2 (0.22)
D10S1710 (124.3 cM)	0.1 (0.28)	0.7 (0.26)
D10S566 (127.1 cM)	0.2 (0.32)	0.7 (0.26)
D10S1671 (127.1 cM)	0.1 (0.36)	2.9 (0.18)
D10S1741 (128.2 cM)	0.3 (0.24)	0.2 (0.32)

Supplemental Table 3. Two-point non-parametric linkage scores (Zlr) and p-values. Families were considered 'late-onset' if all sampled affecteds had onset ages 65 years. Families were considered 'APOE e4/4-negative' if no affected family-member carried the e4/4 genotype. Marker locations in Kosambi cM according to the Marshfield map.
Marker (location)	All families Zlr(p)	Late-onset Zlr (p)	APOE e4/4-negative Zlr (p)
D10S1225 (80.8 cM)	0.9 (0.2)	1.6 (0.06)	0.71 (0.24)
D10S564 (112.6 cM)	0 (1.0)	0 (1.0)	0 (1.0)
D10S583 (115.3 cM)	3.0 (0.0015)	2.8 (0.0025)	2.5 (0.006)
D10S1710 (124.3 cM)	2.4 (0.008)	2.8 (0.003)	2.2 (0.014)
D10S566 (127.1 cM)	1.8 (0.035)	1.5 (0.06)	2.1 (0.02)
D10S1671 (127.1 cM)	3.3 (0.0005)	3.8 (<0.0001)	3.7 (<0.0001)
D10S1741 (128.2 cM)	1.3 (0.09)	0.9 (0.2)	0.8 (0.2)

Supplemental Table 4. Multipoint non-parametric linkage scores (Zlr) and p-values. Families were considered 'late-onset' if all sampled affecteds had onset ages 65 years. Families were considered 'APOE e4/4-negative' if no affected family-member carried the e4/4 genotype. Marker locations in Kosambi cM according to the Marshfield map.
Marker (location)	All families Zlr (p)	Late-onset Zlr (p)	APOE e4/4-negative Zlr (p)
D10S1225 (80.8 cM)	0.9 (0.2)	1.6 (0.06)	0.9 (0.2)
D10S564 (112.6 cM)	0.4 (0.4)	0.5 (0.3)	0.6 (0.3)
D10S583 (115.3 cM)	1.1 (0.15)	1.3 (0.1)	1.3 (0.1)
D10S1710 (124.3 cM)	1.9 (0.029)	2.1 (0.02)	2.15 (0.016)
D10S566 (127.1 cM)	1.6 (0.05)	1.8 (0.03)	2.0 (0.02)
D10S1671 (127.1 cM)	1.3 (0.1)	1.6 (0.05)	1.7 (0.05)
D10S1741 (128.2 cM)	1.2 (0.1)	1.6 (0.06)	1.4 (0.08)

Supplemental Table 5. Autosomal dominant model, maximum two-point parametric LOD scores (Zmax) and recombination fractions (R). 'Myers-positive' (n = 188) if all sampled affected individuals were included in the analyses of Myers et al. (5), 'Myers-negative' (n = 247) otherwise. Marker locations in Kosambi cM according to the Marshfield map. Note that the present study used full families in contrast to only affected sibpairs in Myers et al. (5).
Marker (location)	Myers-positive Zmax (R)	Myers-negative Zmax (R)
D10S1225 (80.8 cM)	0.5 (0.25)	0.1 (0.35)
D10S564 (112.6 cM)	0 (0.40)	0 (0.50)
D10S583 (115.3 cM)	2.3 (0.20)	1.2 (0.23)
D10S1710 (124.3 cM)	1.4 (0.20)	0 (0.40)
D10S566 (127.1 cM)	0.6 (0.24)	0.3 (0.30)
D10S1671 (127.1 cM)	2.7 (0.15)	0.4 (0.29)
D10S1741 (128.2 cM)	0.4 (0.25)	0.1 (0.35)