Fannie Mae and Freddie Mac have a friend on West 57th Street. That’s the New York address of Metacapital Management LP, the hedge fund founded by Deepak Narula.

The much-maligned mortgage aggregators were taken over by the federal government in 2008 and have since absorbed $140 billion in taxpayer bailout money. The head of the House Financial Services Committee wants to abolish them. Yet they still own or guarantee more than half of all U.S. housing loans -- and for that reason, the administration of President Barack Obama isn’t about to let them go belly up.

Narula, 49, has used Fannie and Freddie to build the world’s most-successful hedge fund. His Metacapital Mortgage Opportunities Fund, which invests heavily in agency mortgages, returned 37.8 percent in the first 10 months of 2012, putting it at the top of the Bloomberg Markets list of the 100 best- performing hedge funds managing $1 billion or more, which will be published in the February issue of Bloomberg Markets. That comes on top of a 23.6 percent return in 2011. The Mortgage Opportunities fund is up 520 percent since it started trading in July 2008.

Three of the top five funds in the Bloomberg Markets list invested in mortgage securities, and two of them are run by Minnetonka, Minn.-based Pine River Capital Management LP. Betting on mortgage securities outpaced every other strategy, with an average return of 20.2 percent, against an industry average of just 1.3 percent, according to data compiled by Bloomberg.

SAC Most Profitable
The most-profitable fund in the first 10 months of 2012 was Steve Cohen’s SAC Capital International, which earned $789.5 million for its managers. In November, the U.S. Securities and Exchange Commission notified Cohen’s $14 billion firm, Stamford, Connecticut-based SAC Capital Advisors LP, that it was considering suing it for civil fraud related to insider trading.

Narula’s edge in 2012 was in reading the tea leaves of Washington policy makers. Toward the end of 2011, government-backed mortgage securities dropped in value as Obama expanded programs to help owners refinance and bonds without insurance fell amid the euro crisis.

Narula took advantage. He later concluded that the Federal Reserve was going to help homeowners and bought bonds ahead of its September announcement that it would buy $40 billion a month of agency -- that is, Fannie-, Freddie- and Ginnie Mae-backed -- mortgage bonds.

Following the Fed
“To revive the housing market, the Fed has thrown a lot of firepower at agency mortgage-backed securities,” Narula says. “Policy makers have worked hard to let homeowners refinance. They’ve been clear that that’s their mission -- and you want to be careful going against that mission.”

In addition to his intuition on Washington policy moves, Narula uses mathematical models to calculate how long homeowners will make payments at their current interest rates before either refinancing or defaulting. The models predict behavior based on a homeowner’s credit score, address, loan size, loan age and other factors. The algorithms also allow sophisticated investors to hedge against wrong-way bets.

“You want to come up with wagers where if you’re right, you’ll do really well and if you are wrong, you don’t get hurt too badly,” Narula says.

No. 1 Metacapital is followed on the list by Steve Kuhn’s Pine River Fixed Income Fund, which also invests in mortgage bonds and returned 32.9 percent. Pine River captured No. 2 and No. 4 and tied for No. 19. That fund is run by portfolio manager Aaron Yeary. CQS Directional Opportunities, run by Michael Hintze’s London-based CQS U.K. LLP, was No. 3 and the top European fund. Crispin Odey’s London-based Odey European was second best in Europe, with a 24.1 percent return.

Coleman No. 12
Odey is a stock picker, as is Internet investor Chase Coleman, whose Tiger Global fund was No. 1 in 2011. It fell to No. 12 in 2012, with a 21 percent return. Coleman was the only protege of Julian Robertson, founder of Tiger Management LLC, to crack the top 20. “Tiger cub” Lee Ainslie of Maverick Capital Management saw his No. 31 Maverick fund gain 16.0 percent. Ainslie benefited from wagers on Apple Inc., which returned 47.6 percent as of Oct. 31.

David Tepper also made money on stocks. His Palomino fund, at 24 percent, ties for No. 6 in 2012; it was No. 1 in 2009.

The No. 1 midsize fund, with assets from $250 million to $1 billion, is Cheyne Total Return Credit, operated by London-based Cheyne Capital Management. It boasted a 61.4 percent return.

Hedge Underperformance
Those big gains came amid a fourth consecutive year of underperformance by hedge funds. The average return of 1.3 percent compared with a 14 percent gain, including dividends, for the Standard & Poor’s 500 Index through October.

Since Jan. 1, 2009, the average hedge fund gained a cumulative 13.5 percent compared with 69.8 percent for the S&P 500.

“Hedge funds probably oversold themselves for a long time, saying we’re going to get stock-like returns with lower volatility,” says Andrew Junkin, senior consultant at Wilshire Associates, which advises pension plans. “Then 2008 comes and blows those two myths out of the water. We compare their returns to 60/40 stocks and bonds, and over the last five years I’m paying a lot of money for something that really has not delivered.”

Poor returns forced an estimated 635 hedge funds to close in the first nine months of 2012, 8.5 percent more than a year earlier, according to Chicago-based Hedge Fund Research Inc.

Some big-name managers threw in the towel. Thomas Steyer, founder of $20 billion hedge fund Farallon Capital Management LLC in San Francisco, retired at the end of 2012 to focus on public service. Boston Red Sox co-owner and hedge-fund manager John Henry closed his Florida-based John W. Henry & Co. and returned assets to investors.

Moore Giveback
Other titans also returned money. In August, Moore Capital Management LLC founder Louis Moore Bacon said he would give back $2 billion, or 25 percent, of his flagship hedge fund’s assets because he couldn’t achieve the returns he had historically produced.

Narula attributes his success to long years of studying the bond markets. The son of an Indian diplomat, he earned an engineering degree from the Indian Institute of Technology in Kanpur, one of the country’s top schools. His real interest, however, was finance, and in 1985, he enrolled at Columbia Business School in New York, where he earned a Ph.D. in management science while also studying finance. He then spent 11 years as a mortgage bond analyst and trader at Lehman Brothers Holdings Inc.

Narula started Metacapital in 2002 with $15 million from friends and his own savings. In that year, he gained 17 percent while the S&P 500 fell 23 percent. Investors came running.

Narula saw the danger in the market for subprime mortgages as early as 2005 and started shorting them. His fund suffered when valuations kept rising, and investors headed for the door. In 2006, Narula returned $500 million, and in 2007 he closed the fund.

“We had the right idea in shorting the subprime,” he says, waving his arm in the direction of his 12-member team sitting in front of computer terminals in his sparsely furnished Manhattan office. “If you are too early, you are wrong.”

Narula launched his Mortgage Opportunities Fund in 2008 and has thrived on buying and selling agency-backed mortgages while keeping a close eye on the Fed.

“The Fed’s mission is to drive down the 30-year mortgage rate,” Narula says.

China Connection
At Pine River, Steve Kuhn has taken advantage of his Chinese connection. The firm opened an office in Beijing in 2010 that employs a squad of 33 quantitative analysts and software developers.

Kuhn plays in markets where Narula has a smaller footprint. He buys and sells nonagency mortgage bonds -- that is, those not bought or backed by Fannie and Freddie. He uses several stratagems to hedge against a decline in their value.

To determine which securities to buy, Kuhn and his team analyze massive amounts of data on servicers and borrowers, from credit scores and loan age to ZIP codes and income.

Kuhn is now cutting his holdings in the subprime mortgage market. Narula, by contrast, thinks he can glean hefty returns from agency bonds for several more years.

Others think the game is just about up.

“Our expectations are much more muted,” says John Bailey, chief executive officer at Spruce Private Investors LLC in Stamford, Connecticut, which advises clients on alternative investments. “The easy money’s been made.”

Most-Profitable
Our ranking of the most-profitable funds took 2011 performance numbers into account because most managers get paid only when the value of their funds is greater than its previous highest value. About half of the top-performing large hedge funds had negative returns in 2011. The profits for these funds were calculated by using the percentage by which their return this year exceeded their “high-water mark.”

Several funds appearing on the most-profitable ranking do not show up on our lists of top performers. That is because the size of a fund can trump returns in calculating profits.

We couldn’t obtain returns from several of the biggest hedge-fund firms by assets. For a handful of other firms, we had returns on only one or two funds. Onshore and offshore assets and returns were combined for a number of funds, while figures for other funds on our lists were for only the larger class of the fund.

The numbers were difficult to verify. Unless the information came from Bloomberg or the hedge-fund firm itself, we tried to verify it with other sources.