Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

Table 1 Dark and camouflaged regions vary by genome build. We identified dark and camouflaged regions throughout the genome for three different builds, including GRCh37, GRCh38, and GRCh38+alt, across five different sequencing technologies (or read lengths for Illumina). Specifically, we measured dark regions for Illumina based on 100-nucleotide read lengths, Illumina based on 250-nucleotide read lengths, 10x Genomics, PacBio, and Oxford Nanopore Technologies (ONT). Here, the counts for dark and camouflaged regions are combined. We found that the number of dark regions and nucleotides, both within gene bodies (represented as GB in the table) and outside gene bodies, varies dramatically by build and technology. Overall, each technology has its respective strengths. GRCh38 including alternate contigs has > 3x more dark nucleotides than GRCh37, and more than 2x more dark regions. Results presented throughout the manuscript are based on GRCh38 (in gray)

Dark regions	GRCh37					GRCh38					GRCh38+alt
Dark regions	il100	il250	10x	PacBio	ONT	il100	il250	10x	PacBio	ONT	il100	PacBio	ONT
Non-GB nucs.	22.4M	15.7M	5.4M	11.1M	6.7M	68.7M	42.5M	57.0M	56.8M	52.1M	88.4M	69.5M	59.1M
Non-GB regs.	38,931	16,247	17,481	10,615	13,441	84,174	54,418	20,650	20,276	23,613	91,263	35,136	25,682
GB nucs.	16.3M	11.4M	4.2M	6.7M	3.7M	15.1M	12.2M	4.3M	6.4M	3.3M	41.6M	26.9M	16.2M
GBs	5857	4424	3828	2095	4454	6054	4227	3993	2170	4465	7396	3332	4465
Protein-coding	3792	2814	2845	1251	3464	3804	2437	2875	1275	3406	4291	1741	3041
Pseudogenes	1134	955	454	483	417	1232	1080	518	474	425	1701	876	668
lincRNAs	732	492	398	254	476	753	513	459	284	546	920	417	529
Others	199	163	131	107	97	265	197	141	137	88	484	298	227
GB regions	37,874	20,030	15,076	9729	9757	36,794	21,052	14,878	8999	8701	59,703	29,302	20,657
Intronic	28,751	13,971	11,700	6632	8000	27,982	14,405	11,322	6126	7371	41,219	18,842	14,029
ncRNA exons	4188	2799	1052	1734	959	4351	3396	1216	1738	878	6589	3573	2117
CDS	2657	1836	1313	731	416	2855	2221	1452	766	222	7885	4754	2952
5′UTR	1106	613	617	258	132	908	518	580	191	90	2238	1221	861
3′UTR	1135	785	381	369	233	698	512	307	178	140	1769	910	695
Other UTR	37	26	13	5	6	0	0	1	0	0	3	2	3
Total nucs.	38.7M	27.1M	9.6M	17.8M	10.4M	83.8M	54.7M	61.3M	63.2M	55.4M	130.0M	96.4M	75.3M
Total regs.	76,805	36,277	32,557	20,344	23,198	120,968	75,470	35,528	29,275	32,314	150,966	64,438	46,339

ISSN: 1474-760X