All mutations described in supplementary table 2 are somatic
mutations. GenBank (June 25th 2007) and Ensembl build 45_36g
transcripts were used for annotation. A ranking system was developed
to select transcript/gene for annotating each variant. Prioritization
is based on transcript status (eg. validated over unknown), variant
classification (eg. missense over silent), and other features
(eg. longer protein length over shorter protein length).

An additional germline L858R mutation was identified in EGFR in tumor:
normal pair 16606:16605 but was not included because of its status.

November 4th 2008 update: FLT1 ins allele (sample: 16678; position:
27793650) has been reverse complemented to "A".

November 6th 2008 update:

ENST00000369065 was in Ensembl build 46 and now has been
withdrawn. This affects the annotation of line 253 in supplementary
table 2.

November 8th update:

ENST00000354862 has been UPDATED and should be NAT6. This affects the
annotation of line 315 in supplementary table 2.

ENST00000371701(http://www.ensembl.org/Homo_sapiens/idhistoryview?transcript=ENST00000371701)
has been withdrawn from Ensembl. This affects the annotation of line
603 in supplementary table 2.

ENST00000354647
(http://www.ensembl.org/Homo_sapiens/idhistoryview?transcript=ENST00000354647)
has been withdrawn from Ensembl. This affects the annotation of lines
816 and 817 in supplementary table 2.

New annotations using currently available transcripts for the 5
affected mutations are listed in the last three columns (see
below). chr2:122473483 mutation is no longer within available Ensembl
transcripts.

IFRD2	7866	3	50309166	50309166	Missense	SNP	-	ENST00000354862	p.P266S	c.796	G	16640	A	G	16639	G	G	-	Validated	probably_damaging	 -	 -	Novel: No Cosmic File	Novel: Amino Acid	ENST00000354862 has been UPDATED and should be NAT6 		intronic	ENST00000066014	NULL
FGFR2	2263	10	122473483	122473483	Missense	SNP	-	ENST00000369065	p.R785K	c.2354	C	17060	C	T	17089	C	C	Verified	Validated	benign	 tolerated<>1.00	 -	Novel: Amino Acid	Novel: Amino Acid	ENST00000369065 was in Ensembl build 46 and now has been withdrawn				
NOTCH1	4851	9	138509250	138509250	Missense	SNP	-	ENST00000371701	p.G89C	c.265	C	17308	A	C	17307	C	C	Verified	Validated	probably_damaging	 -	 -	Novel: Amino Acid	Novel: Amino Acid	ENST00000371701 http://www.ensembl.org/Homo_sapiens/idhistoryview?transcript=ENST00000371701 has been withdrawn from Ensembl 		3_prime_untranslated_region	ENST00000277541	NULL
SEMA3B	7869	3	50286866	50286866	Missense	SNP	-	ENST00000354647	p.R400L	c.1199	G	17042	G	T	17071	G	G	Verified	Validated	-	 deleterious<>0.02	 -	Novel: No Cosmic Amino Acid	Novel: Amino Acid	ENST00000354647 http://www.ensembl.org/Homo_sapiens/idhistoryview?transcript=ENST00000354647 has been withdrawn from Ensembl 		Silent_Mutation	ENST00000316347	p.A401
SEMA3B	7869	3	50286980	50286980	Missense	SNP	-	ENST00000354647	p.P438L	c.1313	C	17210	C	T	17209	C	C	Verified	Validated	-	 deleterious<>0.00	 -	Novel: No Cosmic Amino Acid	Novel: Amino Acid	ENST00000354647 http://www.ensembl.org/Homo_sapiens/idhistoryview?transcript=ENST00000354647 has been withdrawn from Ensembl 		Silent_Mutation	ENST00000316347	p.A439