Comprehensive genetic and epigenetic analysis of sporadic meningioma for macro-mutations on 22q and micro-mutations within the NF2 locus

Hansson, Caisa M; Buckley, Patrick G; Grigelioniene, Giedre; Piotrowski, Arkadiusz; Hellström, Anders R; Mantripragada, Kiran; Jarbo, Caroline; Mathiesen, Tiit; Dumanski, Jan P

doi:10.1186/1471-2164-8-16

Table 1 Genetic alterations in one hundred meningiomas.

From: Comprehensive genetic and epigenetic analysis of sporadic meningioma for macro-mutations on 22q and micro-mutations within the NF2 locus

Sample ID	Subtype¹	CH₃	NF2 gene mutations			DNA copy number profiles ⁴
			Position	Mutation²	Assumed effect³	Chromosome 22	Chromosome 1	Loss of non-22 genes⁵
M26	A		Ex 2	227_240del	Lys76fs	Monosomy	Monosomy	D1, S1A, S1B
M71	A		Ex8	810+2T>C	Abn. Spl.	Monosomy	1p, 120.8 Mb TD	D1, P2A, S1A, S1B
M38	A		Ex6	573del; 575_581del	Trp191fs	Monosomy	1p 107.9 Mb TD	P1B, P2A, S1A, S1B
M43	A		Ex12	1185del	Lys396fs	Monosomy	1p 120.3 Mb TD, 4.4 Mb A
M46	A		Ex8	810+2T>C	Abn. Spl.	NAD	NAD
M33	A			NAD		30.6 Mb TD [AC009516-AC002055]	1p, 90.2 Mb TD, 45.8 Mb ID
M9	A			NAD		NAD	NAD
M20	A			NAD		NAD	NAD
M13	F		Ex 2	240+2T>C	Abn. Spl.	Monosomy	1p, 142.9 Mb TD	P2A, S1A, S1B
M88	F		Ex4	364-1G>A	Abn. Spl.	Monosomy	1p 84.1 Mb TD; 1q 4.6, 7.1 Mb IDs, 12.5 Mb TD	P2A
M3	F		Ex 2	240+2T>C	Abn. Spl.	Monosomy	1p 119.8 Mb TD
M14	F		Ex3	249del	His84fs	Monosomy	1p 120.2 Mb TD
M15	F		Ex8	683del	Lys228fs	Monosomy	1p 116.0 Mb TD
M39	F		Ex8	810+1G>A	Abn. Spl.	Monosomy	NS
M42	F		Ex10	995del	Lys332fs	Monosomy	NS
M70	F		Ex6	599+1G>A	Abn. Spl.	Monosomy	NS
M91	F		Ex 2	154del	Arg52fs	Monosomy	NS
M102	F		Ex9	865A>T	Lys289X	Monosomy	NS
M115	F		Ex7	634C>T	Gln212X	NAD	1p 119.6 Mb TD
M64⁶	F			NAD		30.4 Mb TD [AC008079-AC002055], NF2 biallelic del [AC005529]	1p 98.8 Mb ID; 1q 24.2 Mb ID	P1B, P2A
M66	F			NAD		Monosomy	1p 118.1 Mb TD	P2A
M11⁷	F			NAD		0.55, 2.8, 4.5 Mb IDs [U07000-AP00034, AC005004-Z69907, AL022311-Z83851]; 5.9 Mb TD [Z93244-AC002055]	1p 116.8 Mb TD, 3.6 Mb A
M32	F			NAD		5.3 Mb ID [AL022329-AL022336], 15.2 Mb TD [AL009049-AC002055]	NS	D1
M4	F			NAD		Monosomy	NAD
M29	F			NAD		Monosomy	NS
M41	F			NAD		Monosomy	NS
M92	F			NAD		Monosomy	NS
M114	F			NAD		18.0 Mb ID [AP000525-Z68324]	NS
M119	F			NAD		NAD	NS
M10	M		Ex13	1341-2A>G	Abn. Spl.	Monosomy	1p 120.3 Mb TD	P2A
M23	M		Ex3	241-2A>C	Abn. Spl.	Monosomy	1p 120.9 Mb TD	P2A
M67	M		Ex4	432C>A	Tyr144X	Monosomy	1p 120.8 Mb TD	P2A
M98	M		Ex14	1519_1520del	Phe507fs	Monosomy	NAD	D1, P2A, S1A, S1B
M57	M		Ex 2	133_144 del	Asp45fs	Monosomy	NS
M72	M		Ex7	634C>T	Gln212X	Monosomy	NS
M40	M			NAD		Monosomy	1p 164.9 Mb TD	P1B, P2A
M76	M			NAD		Monosomy	1p 142.7 Mb TD	P2A
M105	M			NAD		Monosomy	1p 116.3 Mb TD	P1B, P2A
M34⁸	M			NAD		20.0 Mb TD [AC004542-AC002055]	1p 102.8 Mb ID
M44	M			NAD		Monosomy	1p 85.4 Mb TD
M101	M			NAD		25.1 Mb ID [AP000525-AL035450], 7.9 Mb TD [AL049758-AC002055]	Monosomy, 1p 2.1 Mb R
M30	M			NAD		Monosomy	NAD	D1, P2A
M112	M			NAD		NAD	1p 114.2 Mb TD
M2	M			NAD		NAD	NAD
M5	M			NAD		NAD	NAD
M77	M			NAD		NAD	NAD
M82	M			NAD		NAD	NAD
M45	M			NAD		NAD	NS
M51	M			NAD		NAD	NS
M54	M			NAD		NAD	NS
M61	M			NAD		NAD	NS
M63	M			NAD		NAD	NS
M65	M			NAD		NAD	NS
M69	M			NAD		NAD	NS
M86	M			NAD		NAD	NS
M95	M			NAD		NAD	NS
M99	M			NAD		NAD	NS
M107	M			NAD		NAD	NS
M108	M			NAD		NAD	NS
M111	M			NAD		NAD	NS
M116	M			NAD		NAD	NS
M120	M			NAD		NAD	NS
M93	P		Ex8	810G>T	Glu270Asp	Monosomy	1p 114.3 Mb ID	P2A
M22⁹	P		Ex13, inter1	1390del; 28309611 C>A	Ala464fs, unknown	Monosomy	NS
M62	P			NAD		Monosomy	NS
M21	P			NAD		NAD	NS
M60	T		Ex14	1519_1528del	Phe507fs	Monosomy	1p 118.2 Mb TD	P2A
M1	T		Ex7	650del	Tyr217X	Monosomy	1p 65.0 Mb TD
M31	T		Ex13	1325del	Ala451fs	Monosomy	1p 53.2, 36.3 Mb IDs
M58	T		Ex 2	115-3G>C	Abn. Spl.	30.1 Mb TD [AC007050-AC002055]	1p 120.2 Mb TD
M90	T		Ex3	241-2A>G	Abn. Spl.	20.1Mb ID [AP000525-AL079295], 13.4 Mb TD [AL049850-AC002055]	1p 83.3 Mb TD
M96	T		Ex12	1175G>T	Glu392X	2.0 Mb ID [AP000525-AC007666], 5.4 Mb A [AC006285-AC000102], 27.5 Mb TD [U07000-AC002055]	1p 43.3 Mb TD, 1q 69.9 Mb TD
M52	T		Ex4	431_432insAA	Tyr144X	Monosomy	NS	P1B
M113	T		Ex4	377del	Leu127X	Monosomy	NAD	D1, P1B, P2A, S1A, S1B
M18	T		Ex12	1198C>T	Gln400X	Monosomy	NS
M37	T		Ex8	745_755del	Arg249fs	Monosomy	NS
M48	T		Ex 1	36_37del	Leu14fs	Monosomy	NS
M75	T		Ex8	750del	Thr251fs	Monosomy	NS
M87	T		Ex4	436G>A	Val146Ile	NAD	NS
M56	T			NAD		Monosomy	1p 116.5 Mb TD	P2A
M85	T			NAD		Monosomy	1p 108.2 Mb TD	P2A
M109	T			NAD		5.7 Mb A [AC006548-AC007957], 30.6 Mb TD [AC009516-AC002055]	1p 120.2 Mb TD
M27	T			NAD		15.5Mb ID [AP000525-AC005005], 14.1 Mb TD [AL049749-AC002055]	NS
M59	T			NAD		Monosomy	NS
M68	T			NAD		Monosomy	NS
M94	T			NAD		Monosomy	NS
M97	T			NAD		Monosomy	NS
M25	T			NAD		NAD	1p 98.7 Mb TD
M117	T			NAD		NAD	1p 36.1 Mb TD
M104¹⁰	T	+		NAD		NAD	NS
M8	T			NAD		NAD	NS
M12	T			NAD		NAD	NS
M17	T			NAD		NAD	NS
M35	T			NAD		NAD	NS
M55	T			NAD		NAD	NS
M89	T			NAD		NAD	NS
M103	T			NAD		NAD	NS
M78	U		Ex10	999+1G>T	Abn. Spl.	Monosomy	1p 3.8 Mb TD
M79	U			NAD		NAD	1p 39.1Mb ID, 1q 41.3Mb TD
M83	U			NAD		NAD	NS

1 Tumors are grouped according to histopathological subtypes. Abbreviations: A, Anaplastic; F, Fibroblastic; M, Meningothelial; P, Psammomatous; T, Transitional and U, Unclassified.
2 Position of the mutations according to numbering of the cDNA sequence, nucleotide number one is the A in the ATG translation initiation codon [GenBank:AF369658]. Abbreviations: substitution, >; deletion, del; insertion, ins; No Aberration Detected, NAD. Donor splice site mutations indicated by the last nucleotide of the preceding exon, a plus sign and position in the intron (e.g. 240+2T>C). Acceptor splice site mutations denoted by the first nucleotide of the following exon, a minus sign and position in the intron (e.g. 241-2A>C).
3 Amino acid number one is the translation initiator Methionine. Abbreviations: translation termination codon, X; frame shift, fs; abnormal splicing, Abn. Spl.
4 Data from copy number imbalances on chromosome 1 were previously published [34]. Abbreviations: Terminal Deletion, TD; Interstitial Deletion, ID; Amplification/gain, A; Not Studied, NS; No Aberration Detected, NAD; Retained segment R. Genbank accession numbers in squared brackets.
5 Loss of non-chromosome 22 clones spanning the DAL1, D1; PTCH2A, P2A; PTCH1B, P1B; SUFU1A, S1A; and SUFU1B, S1B genes.
6 M64 displays a homozygous deletion of the NF2 gene.
7 M11 demonstrates multiple deletions not affecting the NF2 gene.
8 M34 displays a terminal deletion not affecting the NF2 locus.
9 M22 presents two mutations in the NF2 locus, in exon 13 and in the CNG inter1. The position of the inter1 mutation is according to numbering on chromosome 22 (UCSC Homo sapiens Genome Browser, assembly July 2003). Ten bases on each side of the mutation: agcaaagagaCaaattaccca.
10 Methylation of a single CpG site in the intron 1 of the NF2 gene in ~40% of DNA molecules.

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