Dr. Dulai's Bio 184 section Lab 2.1 notes

Updated: 6 March, 2007

How Phase Contrast Works

Bio 184 Practical 2

RESULTS

	Mother’s Alleles	Child’s Alleles	Obligate Paternal Allele	Alleged Father Mark’s Alleles	Alleged Father Peter’s Alleles	Can Either be Excluded?
Profiler Loci
D3S1358	15,18	18,18		16,18	17,18	No
VWA	16,17	17,19	19	14,17	18,19	Mark
FGA	20,23	22,23	22	22,24	22,24	No
D8S1179	14,14	14,15	15	10,14	14,15	Mark
D21S11	28,29	28,30.2	30.2	28,29	30,30.2	Mark
D18S51	17,17	12,17	12	14,19	12,12	Mark
D5S818	11,13	11,12	12	12,13	11,12	No
D13S317	11,12	8,12	8	11,13	8,12	Mark
D7S820	10,10	10,12	12	7,10	8,12	Mark
Additional Cofiler Loci
D16S539	11,12	9,12	9	10,11	9,12	Mark
THO1	6,9.3	6,9.3		9,9.3	9.3,9.3	No
TPOX	8,11	8,8		9,9	8,8	Mark
CSF1PO	11,11	11,11		10,10	11,13	Mark
Amelogenin	X	XY	XY	XY	XY	No

Paternity Index = Prob. Alleged Father could have contributed obligate paternal allele

Prob. Random Man could have contributed obligate paternal allele

Combined PI = Product of individual PIs at each locus tested

Locus	Obligate Paternal Allele	Freq. Obligate Paternal Allele		PI
D3S1358	18	0.1450	0.5/0.1450	3.45
VWA	19	0.1100	0.5/0/1100	4.55
FGA	22	0.1400	0.5/0.1400	3.57
D8S1179	15	0.1300	0.5/0.1300	3.85
D21S11	30.2	0.0250	0.5/0.0250	20
D18S51	12	0.1425	1/0.1425	7.02
D5S818	12	0.3325	0.5/0.3325	1.50
D13S317	8	0.1150	0.5/0.1150	4.35
D7S820	12	0.1600	0.5/0.1600	3.13
D16S539	9	0.1075	0.5/0.1075	4.65
THO1	9.3	0.3500	1/0.3500	2.86
THOX	8	0.5825	1/0.5825	1.72
CSF1PO	11	0.2575	0.5/0.2575	1.94
Combined PI				2.75*10^7

*At each locus, the likelihood that the alleged father could have contributed the obligate paternal allele is either 0.5 (if he is a heterozygote) or 1.0 (if he is homozygote).

PI = p(alleged father contributed alleles)/p(random man contributed)

CPI = product of all PI [1]

____________________________

PRM = 2pq for Heterozygotes (formula 1)

= p^2 + [p(1-p)(0.01)] for HOMOzygotes (formula 2)

Profiler Loci	Child Homo/Hetero	Alleles	Formula used	Value
D3S1358	HOMO	18, 18	2	0.02226
VWA	Hetero	17, 19	1	0.055
FGA	Hetero	22, 23	1	0.0392
D8S1179	Hetero	14, 15	1	0.04875
D21S11	Hetero	28, 30.2	1	0.008125
D18S51	Hetero	12, 17	1	0.029925
D5S818	Hetero	11, 12	1	0.2610125
D13S317	Hetero	8, 12	1	0.064975
D7S820	Hetero	10, 12	1	0.0768
Additional Cofiler Loci
D16S539	Hetero	9, 12	1	0.073637
THO1	Hetero	6, 9.3	1	0.17675
TPOX	HOMO	8, 8	2	0.341738
CSF1PO	HOMO	11, 11	2	0.068218
			2.24814E-16

Frequency tables

ALLELE	African-American	Caucasian	D8S1179			Allele	AA	C	Allele	AA	C
ALLELE	African-American	Caucasian	8	*	0.0175	D18S51			D16S539
D3S1358			9	0.0051*	0.01*	16	0.1744	0.14	5	0.0026*	*
9	0.0026*	*	10	0.0308	0.08	17	0.1641	0.105	8	0.0385	0.015
10	*	*	11	0.0436	0.0625	18	0.1103	0.06	9	0.1821	0.1075
11	0.0026*	0.0025*	12	0.1051	0.1425	19	0.1026	0.0375	10	0.1128	0.0425
12	0.0051*	0.0025*	13	0.1974	0.3475	20	0.0487	0.015	11	0.03	0.2975
13	*	0.0050*	14	0.3333	0.1875	21	0.0103*	0.0100*	12	0.1846	0.3425
14	0.118	0.1125	15	0.2103	0.13	22	0.0103*	0.0025*	13	0.1564	0.175
15	0.2795	0.2825	16	0.0641	0.02	23	0.0026*	0.0025*	14	0.0205	0.0175
15.2	0.0026*	*	17	0.0103*	0.0025*	24	*	*	15	0.0026*	0.0025*
16	0.3231	0.2225	18	*	*	25	*	*
17	0.218	0.2225	19	*	*	26	*	*	THO1
18	0.0462	0.145	D21S11						5	0.0026*	*
19	0.0026*	0.0050*	24.2	*	0.0050*	D5S818			6	0.1308	0.2525
vWA			25	*	*	7	0.0026*	0.0025*	7	0.4	0.16
11	0.0026*	*	26	0.0026*	*	8	0.0513	0.0050*	8	0.2282	0.0925
12	*	*	27	0.059	0.0375	9	0.0205	0.0225	9	0.1308	0.1375
13	0.0154	*	28	0.218	0.1625	10	0.0744	0.0675	9.3	0.1	0.35
14	0.077	0.085	28.2	*	*	11	0.2539	0.3925	10	0.0077*	0.0075*
15	0.2205	0.0825	29	0.2	0.2075	12	0.3256	0.3325
16	0.2692	0.1975	29.2	*	0.0050*	13	0.2487	0.165	TPOX
17	0.1692	0.25	29.3	0.0026*	*	14	0.0205	0.0100*	6	0.0821	*
18	0.1385	0.2575	30	0.1615	0.2625	15	0.0026*	*	7	0.0359	*
19	0.0846	0.11	30.2	0.0256	0.025	16	*	0.0025*	8	0.3436	0.5825
20	0.0205	0.015	31	0.0897	0.055				9	0.2	0.1125
21	*	0.0025*	31.2	0.059	0.105	D13S317			10	0.0923	0.0475
22	0.0026*	*	32	0.0077*	0.0125*	5	*	0.0025*	11	0.2154	0.225
FGA			32.2	0.0692	0.0725	8	0.0359	0.115	12	0.0308	0.03
16.2	0.0026*	*	33	0.0051*	0.0025*	9	0.0231	0.0775	13	*	0.0025*
17	0.0026*	*	33.1	0.0026*	*	10	0.0231	0.0675
18	0.0051*	0.015	33.2	*	0.0075*	11	0.2718	0.3125	CSF1PO
19	0.0462	0.0625	34	0.0026*	*	12	0.4436	0.2825	6	0.0026*	*
19.2	0.0026*	*	34.2	*	0.0075*	13	0.141	0.0975	7	0.0718	*
20	0.0436	0.1625	35	0.0359	*	14	0.0615	0.0425	8	0.0744	0.0025*
20.2	*	0.0075	35.2	*	*	15	*	0.0025*	9	0.0385	0.0275
21	0.1333	0.1775	36	0.0154	*				10	0.3051	0.2675
21.2	0.0026*	*	38	0.0026*	*	D7S820			10.3	*	0.0025*
22	0.1897	0.14	D18S51			6	0.0051*	*	11	0.2128	0.2575
22.2	0.0026*	0.0050*	9	*	*	6.3	*	0.0025*	12	0.2205	0.3575
23	0.1897	0.14	10	0.0051*	0.0050*	7	*	0.025	13	0.0692	0.07
24	0.1641	0.1325	10.2	0.0051*	*	8	0.1795	0.175	14	0.0051*	0.015
25	0.1231	0.1125	11	0.0154	0.02	9	0.118	0.13	15	*	*
26	0.041	0.015	12	0.0564	0.1425	10	0.3359	0.24
26.2	*	*	13	0.041	0.15	11	0.2282	0.23
27	0.041	0.0050*	13.2	0.0051*	*	12	0.0949	0.16
28	0.0077*	*	14	0.0667	0.1675	13	0.0359	0.0275
29	0.0026*	*	14.2	0.0051*	*	14	0.0026*	0.0075*
30	*	*	15	0.1769	0.1425	15	*	0.0025*