Table 3.

A list of molecularly delimited common fragile sites (CFSs) obtained from a manual search of the literature

FRA	Chr	Start	End	BAC/STS from	BAC/STS to	Type	Frequency	Cancer genes	miRNAs	References
FRA1E	1	97,749,961	98,119,925	RP4-538N4	RP11-128G13	Aphidicolin	Common			[92]
FRA1H	1	216,110,179	226,742,379	RP11-22M7	RP11-118H4	5AZA	Common	TGFB2	hsa-mir-215, hsa-mir-194-1, hsa-mir-664a, hsa-mir-320b-2, hsa-mir-4742, hsa-mir-6741	[154]
FRA2Ccen	2	18,524,760	19,272,430	RP11-720L11	RP11-78J22	Aphidicolin	Common			[97]
FRA2Ctel	2	14,934,889	15,681,539	RP11-526G2	RP11-32P22	Aphidicolin	Common			[97]
FRA2G	2	169,498,510	170,313,244	RP11-285F23	RP11-724O16	Aphidicolin	Common			[155]
FRA2H	2	186,716,111	187,251,132	RP11-561J1	RP11-639N24	Aphidicolin	Common			[156]
FRA3B	3	59,623,632	63,846,635	RP11-70P20	RP11-50F24	Aphidicolin	Common			[157]
FRA4F	4	90,208,191	97,312,924	RP11-549C16	RP11-145G20	Aphidicolin	Common			[109]
FRA6E	6	160,275,245	166,079,958	D6S1581	D6S1719	Aphidicolin	Common			[158]
FRA6F	6	111,577,970	112,568,919	RP5-1112D6	RP1-142L7	Aphidicolin	Common			[159]
FRA6H	6	27,804,038	37,156,663	RP1-193B12	RP11-588I14	Aphidicolin	Common	RXRB, PPARD, CDKN1A	hsa-mir-877, hsa-mir-4640, hsa-mir-6891, hsa-mir-6832, hsa-mir-4646, hsa-mir-1236, hsa-mir-6721, hsa-mir-6833, hsa-mir-3135b, hsa-mir-219a-1, hsa-mir-6873, hsa-mir-6834, hsa-mir-5004, hsa-mir-3934, hsa-mir-7159, hsa-mir-1275, hsa-mir-6835, hsa-mir-7111, hsa-mir-5690, hsa-mir-3925	[115]
FRA7B	7	1	12,392,296	Telomere	RP11-507C1	Aphidicolin	Common	PDGFA, RAC1	hsa-mir-339, hsa-mir-4655, hsa-mir-6836, hsa-mir-4648, hsa-mir-4656, hsa-mir-589, hsa-mir-6874, hsa-mir-3683	[116]
FRA7E	7	80,508,751	84,935,939	D7S1934	SHGC-104456	Aphidicolin	Common	HGF		[117]
FRA7G	7	115,894,865	116,072,877	D7S486	D7S522	Aphidicolin	Common			[160]
FRA7H	7	130,413,791	130,857,950	D7S786	D7S649	Aphidicolin	Common		hsa-mir-29a, hsa-mir-29b-1	[161]
FRA7I	7	144,671,106	146,121,417	SHGC-153624	sWSS2627	Aphidicolin	Common			[120]
FRA7K	7	110,657,856	111,031,412	WI-5281	SHGC-78648	Aphidicolin	Common			[121]
FRA8C	8	124,285,269	128,421,245	RP11-468O2	RP11-382A18	Aphidicolin	Common		hsa-mir-548aa-1, hsa-mir-548d-1, hsa-mir-6844, hsa-mir-4662b, hsa-mir-4662a	[162]
FRA9G	9	17,135,038	17,503,917	Within c9orf39/CNTLN		Aphidicolin	Common			[125]
FRA10F	10	125,391,503	128,256,865	RP11-391M7	RP11-179O22	Aphidicolin	Common	CTBP2	hsa-mir-4296, hsa-mir-4484	[130]
FRA11E	11	32,086,458	34,028,916	RP1-17K7	RP13-786C16	Aphidicolin	Common			[134]
FRA11G	11	113,688,799	118,157,704	RP11-667M19	RP11-832A4	Aphidicolin	Common	ZBTB16		[133]
FRA13A	13	35,546,088	36,184,897	RP11-307O13	RP11-270C18	Aphidicolin	Common			[139]
FRA13E	13	73,285,774	76,386,498	RP11-342J4	RP11-29G8	Aphidicolin	Common			[115]
FRA16D	16	78,420,359	78,731,553	AH009490.2	FRA16D seq	Aphidicolin	Common			[163]
FRAXB	X	6,595,111	7,548,235	DXS1130	DXS237	Aphidicolin	Common		hsa-mir-4767	[164]

The list of molecularly mapped CFSs was compiled by performing a systematic search of the literature for each one of the known cytogenetically mapped fragile sites (n = 125). Whenever the placement of STS markers or BACs on GRC37/hg19 was unknown, it was verified by megaBLAST (default parameters) of the complete sequence against the human chromosome sequences. Only matches with greater than 90 % coverage were considered for CFS placement. Twenty-six (26) CFSs with a precise mapping were identified (see Table 4), whose coordinates were then mapped to the reference genome version GRC37. Whenever the precise location of BACs was unknown, it was verified by alignment with NCBI Megablast (default settings). The annotation of the reference human genome was obtained from UCSC (URL: hgdownload.cse.ucsc.edu/goldenPath/hg19/) in December 2013. The utility “bigWigSummary” was used to extract mean scores for molecularly mapped fragile regions and randomly selected non-fragile control regions. The BAC/STS limits have been extracted from the cited publication and coordinates mapped on GRC37. Note that FRA2C has been divided into two separate, molecularly defined hotspots