An application of logistic regression model to the study of constitutional imbalances in human chromosomal fragile sites

Figures & data

Table 1: Chromosomal fragile sites (CFSs) information.

Chromosome	Deletion Prop. ${}^{\mathrm{a}}$	Notation of the 237 CFSs
1	0.63 (16,19)	FRA1	FRA1A	FRA1B	FRA1D	FRA1E ${}^{\mathrm{b}}$	FRA1F
		FRA1G	FRA1H	FRA1I	FRA1J ${}^{\mathrm{b}}$	FRA1K	FRA1L
		FRA1M	FRA1N	FRA1O ${}^{\mathrm{b}}$	FRA1P	FRA1Q	FRA1R
		FRA1S
2	0.58 (18,22)	FRA2	FRA2A	FRA2B	FRA2C ${}^{\mathrm{b}}$	FRA2D ${}^{\mathrm{b}}$	FRA2E
		FRA2F	FRA2G	FRA2H ${}^{\mathrm{b}}$	FRA2I	FRA2J	FRA2K
		FRA2L ${}^{\mathrm{b}}$	FRA2M	FRA2N	FRA2O	FRA2P	FRA2Q
		FRA2R	FRA2S	FRA2T	FRA2U
3	0.62 (15,18)	FRA3	FRA3A ${}^{\mathrm{b}}$	FRA3B	FRA3C	FRA3D	FRA3E
		FRA3F	FRA3G	FRA3H	FRA3I ${}^{\mathrm{b}}$	FRA3J	FRA3K
		FRA3L	FRA3M	FRA3N	FRA3O	FRA3P ${}^{\mathrm{b}}$	FRA3Q
4	0.48 (11,14)	FRA4	FRA4B	FRA4A	FRA4C	FRA4D	FRA4E
		FRA4F	FRA4G ${}^{\mathrm{b}}$	FRA4H ${}^{\mathrm{b}}$	FRA4I	FRA4J	FRA4K ${}^{\mathrm{b}}$
		FRA4L	FRA4M
5	0.59 (14,15)	FRA5A	FRA5C	FRA5D	FRA5E	FRA5F	FRA5G
		FRA5H	FRA5I	FRA5J	FRA5K	FRA5L	FRA5M ${}^{\mathrm{b}}$
		FRA5N	FRA5O	FRA5P
6	0.61 (11,13)	FRA6A ${}^{\mathrm{b}}$	FRA6B	FRA6C ${}^{\mathrm{b}}$	FRA6D	FRA6E	FRA6F
		FRA6G	FRA6H	FRA6I	FRA6J	FRA6K	FRA6L
		FRA6M
7	0.57 (10,13)	FRA7A	FRA7B	FRA7C ${}^{\mathrm{b}}$	FRA7D	FRA7E ${}^{\mathrm{b}}$	FRA7F ${}^{\mathrm{b}}$
		FRA7G	FRA7H	FRA7I	FRA7J	FRA7K	FRA7L
		FRA7M
8	0.49 (6,9)	FRA8A	FRA8B ${}^{\mathrm{b}}$	FRA8C	FRA8D	FRA8F ${}^{\mathrm{b}}$	FRA8G
		FRA8H	FRA8I	FRA8J ${}^{\mathrm{b}}$
9	0.58 (9,12)	FRA9A	FRA9B	FRA9D ${}^{\mathrm{b}}$	FRA9F ${}^{\mathrm{b}}$	FRA9G	FRA9H
		FRA9I	FRA9J ${}^{\mathrm{b}}$	FRA9K	FRA9L	FRA9M	FRA9N
10	0.57 (9,10)	FRA10A	FRA10C	FRA10D	FRA10E ${}^{\mathrm{b}}$	FRA10F	FRA10G
		FRA10H	FRA10I	FRA10J	FRA10K
11	0.73 (6,12)	FRA11C ${}^{\mathrm{b}}$	FRA11D ${}^{\mathrm{b}}$	FRA11E ${}^{\mathrm{b}}$	FRA11F	FRA11G	FRA11H ${}^{\mathrm{b}}$
		FRA11J	FRA11K	FRA11L ${}^{\mathrm{b}}$	FRA11M	FRA11N ${}^{\mathrm{b}}$	FRA11O
12	0.49 (9,12)	FRA12A	FRA12B	FRA12C	FRA12D	FRA12E	FRA12F
		FRA12G	FRA12H ${}^{\mathrm{b}}$	FRA12I	FRA12J	FRA12K ${}^{\mathrm{b}}$	FRA12L ${}^{\mathrm{b}}$
13	0.64 (8,8)	FRA13A	FRA13B	FRA13C	FRA13D	FRA13E	FRA13G
		FRA13H	FRA13I
14	0.55 (8,8)	FRA14A	FRA14B	FRA14C	FRA14D	FRA14E	FRA14F
		FRA14G	FRA14H
15	0.61 (8,8)	FRA15	FRA15A	FRA15B	FRA15C	FRA15D	FRA15E
		FRA15F	FRA15G
16	0.62 (7,9)	FRA16A	FRA16C	FRA16D ${}^{\mathrm{b}}$	FRA16E	FRA16F	FRA16G
		FRA16H ${}^{\mathrm{b}}$	FRA16I ${}^{\mathrm{b}}$	FRA16J
17	0.41 (4,5)	FRA17A	FRA17B ${}^{\mathrm{b}}$	FRA17C	FRA17D	FRA17E
18	0.49 (5,6)	FRA18A ${}^{\mathrm{b}}$	FRA18B	FRA18C	FRA18D	FRA18E	FRA18F
19	0.39 (2,3)	FRA19A	FRA19B	FRA19C ${}^{\mathrm{b}}$
20	0.49 (4,6)	FRA20	FRA20A ${}^{\mathrm{b}}$	FRA20B	FRA20C	FRA20D	FRA20E ${}^{\mathrm{b}}$
21	0.57 (3,3)	FRA21	FRA21A	FRA21B
22	0.59 (2,2)	FRA22A	FRA22B
X	0.29 (8,10)	FRAXA	FRAXB	FRAXC ${}^{\mathrm{b}}$	FRAXD	FRAXEF	FRAXG ${}^{\mathrm{b}}$
		FRAXH	FRAXI	FRAXJ	FRAXK

^aDeletion mean proportion, including CFS totals without and with zero deletions or zero duplications in parentheses. ^bZero deletion or zero duplication CFS

Figure 1: Frequency of deletions (top left) and duplications (bottom left) and observed deletion proportion by CFS (right).

Table 2: Statistical inference for logistic regression model $M_R$ (Wald test p-value $<0.05$)–Part one.

						95% C.I. for $\hspace{0.17em}\mathrm{\text{exp}}\hspace{0.17em}(\beta )$
Fragile Site	$\beta$	S. Error	Wald	P-value	$\hspace{0.17em}\mathrm{\text{exp}}\hspace{0.17em}(\beta )$	Lower L.	Upper L.
(Intercept)	0.07	0.035	2.07	0.0380	1.08	1.00	1.15
FRA1A	1.02	0.207	4.95	$<$0.0001	2.79	1.88	4.24
FRA1F	–0.53	0.154	–3.43	0.0006	0.59	0.43	0.80
FRA1I	1.13	0.297	3.81	0.0001	3.10	1.78	5.73
FRA1L	1.18	0.360	3.27	0.0011	3.25	1.67	6.95
FRA1Q	2.45	0.736	3.33	0.0009	11.61	3.45	72.25
FRA1R	2.63	1.033	2.55	0.0108	13.94	2.82	252.1
FRA2I	0.75	0.364	2.06	0.0398	2.11	1.06	4.48
FRA2K	2.49	1.038	2.40	0.0164	12.08	2.40	219.5
FRA2R	–0.85	0.351	–2.41	0.0158	0.43	0.21	0.83
FRA2S	1.87	0.618	3.03	0.0025	6.50	2.24	27.57
FRA2T	1.34	0.373	3.59	0.0003	3.82	1.92	8.46
FRA2U	–1.87	0.765	–2.44	0.0147	0.15	0.02	0.57
FRA3D	1.02	0.473	2.17	0.0301	2.79	1.17	7.70
FRA3J	–2.21	0.530	–4.18	$<$0.0001	0.11	0.03	0.27
FRA3K	2.23	1.049	2.12	0.0337	9.29	1.78	170.6
FRA4	–2.23	0.611	–3.66	0.0003	0.11	0.03	0.31
FRA4D	1.30	0.291	4.45	$<$0.0001	3.65	2.12	6.70
FRA5F	2.07	0.748	2.76	0.0058	7.90	2.26	49.86
FRA5G	–0.93	0.361	–2.58	0.0098	0.39	0.19	0.78
FRA5N	2.01	0.751	2.67	0.0076	7.43	2.11	47.06
FRA6F	1.15	0.510	2.26	0.0241	3.16	1.25	9.63
FRA6M	0.91	0.392	2.31	0.0208	2.48	1.19	5.65
FRA7B	0.65	0.327	2.00	0.0455	1.92	1.03	3.76
FRA7D	–2.23	0.611	–3.66	0.0003	0.11	0.03	0.31
FRA7I	0.67	0.281	2.39	0.0169	1.96	1.14	3.46
FRA7J	–0.67	0.274	–2.43	0.0150	0.51	0.29	0.87

Table 3: Statistical inference for logistic regression model $M_R$ (Wald test p-value $<0.05$)–Part two.

						95% C.I. for $\hspace{0.17em}\mathrm{\text{exp}}\hspace{0.17em}(\beta )$
Fragile Site	$\beta$	S. Error	Wald	p-value	$\hspace{0.17em}\mathrm{\text{exp}}\hspace{0.17em}(\beta )$	Lower L.	Upper L.
FRA8A	–2.07	0.616	–3.35	0.0008	0.13	0.03	0.37
FRA8C	–1.41	0.504	–2.80	0.0052	0.24	0.08	0.61
FRA8I	–2.47	0.739	–3.34	0.0008	0.08	0.01	0.29
FRA9I	1.11	0.406	2.72	0.0065	3.02	1.42	7.15
FRA9K	1.67	0.411	4.06	$<$0.0001	5.31	2.53	12.99
FRA10C	0.76	0.380	2.00	0.0460	2.14	1.04	4.71
FRA10G	0.67	0.274	2.44	0.0147	1.95	1.16	3.40
FRA11F	1.66	0.627	2.65	0.0081	5.26	1.76	22.58
FRA11J	0.59	0.277	2.14	0.0321	1.81	1.06	3.18
FRA11O	1.80	0.538	3.34	0.0008	6.04	2.35	20.50
FRA12D	–3.33	1.020	–3.27	0.0011	0.04	0.00	0.17
FRA12E	–2.68	0.734	–3.65	0.0003	0.07	0.01	0.23
FRA14B	1.54	0.775	1.98	0.0476	4.65	1.22	30.25
FRA14D	1.31	0.458	2.87	0.0041	3.72	1.62	10.05
FRA14H	–0.86	0.239	–3.59	0.0003	0.42	0.26	0.67
FRA15C	0.33	0.165	2.01	0.0446	1.39	1.01	1.93
FRA16E	1.43	0.392	3.64	0.0003	4.18	2.04	9.71
FRA16F	0.84	0.162	5.20	$<$0.0001	2.32	1.70	3.21
FRA16J	1.61	0.488	3.30	0.0010	5.02	2.10	14.83
FRA17C	–0.84	0.217	–3.88	0.0001	0.43	0.28	0.65
FRA17D	–0.43	0.158	–2.74	0.0062	0.65	0.48	0.88
FRA17E	–0.74	0.277	–2.67	0.0075	0.48	0.27	0.81
FRA18B	1.91	0.535	3.57	0.0004	6.74	2.64	22.75
FRA18C	2.26	0.606	3.73	0.0002	9.60	3.42	40.05
FRA19A	0.80	0.194	4.10	$<$0.0001	2.22	1.53	3.27
FRAXB	–1.09	0.198	–5.49	$<$0.0001	0.34	0.23	0.49
FRAXEF	–1.96	0.300	–6.55	$<$0.0001	0.14	0.07	0.24
FRAXH	–0.57	0.214	–2.65	0.0081	0.57	0.37	0.86
FRAXI	–1.87	0.625	–2.99	0.0028	0.15	0.04	0.46

Figure 2: Chromosomal fragile site effects in the log-odds of deletion: estimates and 95% confidence intervals (CI).

Data availability statement

The data that support the findings of this study are available from the corresponding author, [Prata Gomes], upon reasonable request.