This version represents the May 2004 human reference sequence of NCBI Build 35 for chromosome 16 and the resultant gene catalog.

The final version of the tiling path contains 618 bacterial artificial chromosomes (BACs), 79 cosmids, seven fosmids, five phage-derived artificial chromosomes (PACs), three yeast artificial chromosome (YAC) subclones, two P1 phages, two phage vectors and five genomic polymerase chain reaction (PCR) fragment that span the euchromatin regions of both the p and q arms. The chromosome is represented with only 4 gaps remaining, with two in each of the chromosome arms. The clone map is estimated to cover 99.9% of the euchromatic sequence.

Sequence was generated using a clone-by-clone shotgun sequencing strategy followed by finishing using a custom primer approach. Recalcitrant areas or hard gaps were closed with additional sequence data derived from transposon sequencing, small insert shatter libraries or PCR. One of the gaps is found in the highly duplicated pericentromeric region in the p arm, while two of the remaining non-pericentromeric gaps are resistant to stable cloning with conventional vectors, and efforts are ongoing to close the estimated ,25 kilobases (kb) of missing sequence using alternative vector. The final gap is found near the telomere of the q arm in a region of subtelomeric repeats distal to the last identifiable cosmid subclone (AC137934) of a 16q telomere half-YAC.

On the basis of internal and external quality checks, we estimate the accuracy of our finished sequence to exceed 99.99%. In total, we finished 78,884,754 base pairs and estimate the total size of the chromosome, including the four clone gaps and the recalcitrant centromere and its adjacent heterochromatic portion of the q. arm, sized together at 9.8 megabases (Mb) the total size of the chromosome is estimated at 88.7Mb.

The finished sequence is estimated to cover 99.9% of the euchromatic sequence and to have captured all known genes that were previously mapped to chromosome 16.

Gene Catalog.

We placed gene model transcripts on the chromosome 16 genomic sequence and manually reviewed a total of 880 protein-coding regions as gene loci. These loci contain 1,670 full-length (or nearly full-length) transcripts, including partial (EST) evidence for 208 additional splice variants.

Jeremy Schmutz¹, Joel Martin², Astrid Terry², Olivier Couronne³, Jane Grimwood¹, Steve Lowry², Laurie A. Gordon^4,2, Duncan Scott², Gary Xie^5,2, Wayne Huang², Uffe Hellsten², Mary Tran-Gyamf^4,2, Xinwei She⁶, Shyam Prabhakar³, Andrea Aerts², Michael Altherr^5,2, Eva Bajorek¹, Stacey Black¹, Elbert Branscomb^4,2, Chenier Caoile¹, Jean F. Challacombe⁵, Yee Man Chan¹, Mirian Denys¹, Chris Detter², Julio Escobar¹, Dave Flowers¹, Dea Fotopulos¹, Tijana Glavina², Maria Gomez¹, Eidelyn Gonzales¹, David Goodstein², Igor Grigoriev², Matthew Groza⁴, Nancy Hammon², Trevor Hawkins², Lauren Haydu¹, Sanjay Israni², Jamie Jett², Kristen Kadner², Heather Kimball², Arthur Kobayashi^2,4, Frederick Lopez¹, Yunian Lou², Diego Martinez², Catherine Medina¹, Jenna Morgan², Richard Nandkeshwar⁴, James P. Noonan⁷, Sam Pitluck², Martin Pollard², Paul Predki², James Priest³, Lucia Ramirez¹, Sam Rash², James Retterer¹, Alex Rodriguez¹, Stephanie Rogers¹, Asaf Salamov², Angelica Salazar¹, Nina Thayer^5,2, Hope Tice², Ming Tsai¹, Anna Ustaszewska², Nu Vo¹, Jeremy Wheeler¹, Kevin Wu¹, Joan Yang¹, Mark Dickson¹, Jan-Fang Cheng³, Evan E. Eichler⁶, Anne Olsen^4,2, Len A. Pennacchio^3,2, Daniel S. Rokhsar², Paul Richardson², Susan M. Lucas², Richard M. Myers¹, Edward M. Rubin^3,2

1. Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA

2. DOE’s Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA

3. Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA

4. Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA

5. Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA

6. Department of Genetics, Center for Computational Genomics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA

7. Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA